Hot-fix --version-check.

bin/pt-archiver

@@ -4977,10 +4977,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -5015,7 +5032,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-config-diff

@@ -4682,10 +4682,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -4720,7 +4737,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-deadlock-logger

@@ -3747,10 +3747,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -3785,7 +3802,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-diskstats

@@ -4351,10 +4351,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -4389,7 +4406,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-duplicate-key-checker

@@ -4323,10 +4323,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -4361,7 +4378,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-find

@@ -3135,10 +3135,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -3173,7 +3190,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-fk-error-logger

@@ -3257,10 +3257,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -3295,7 +3312,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-heartbeat

@@ -4303,10 +4303,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -4341,7 +4358,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-index-usage

@@ -5778,10 +5778,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -5816,7 +5833,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-kill

@@ -6032,10 +6032,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -6070,7 +6087,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-online-schema-change

@@ -7062,10 +7062,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -7100,7 +7117,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-query-digest

@@ -12030,10 +12030,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -12068,7 +12085,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-slave-delay

@@ -3653,10 +3653,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -3691,7 +3708,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-slave-restart

@@ -4302,10 +4302,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -4340,7 +4357,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-table-checksum

@@ -905,10 +905,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -943,7 +960,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-table-sync

@@ -9140,10 +9140,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -9178,7 +9195,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-upgrade

@@ -4058,10 +4058,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -4096,7 +4113,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

bin/pt-variable-advisor

@@ -4560,10 +4560,27 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -4598,7 +4615,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }

lib/VersionCheck.pm

@@ -249,10 +249,33 @@ sub update_check_times {
    my $vc_file   = $args{vc_file} || version_check_file();
    PTDEBUG && _d('Updating last check time:', $now);
 
+   # We need to write back all instances to the file.  The given
+   # instances are the ones updated, so use the current ts (now).
+   my %all_instances = map {
+      $_->{id} => { name => $_->{name}, ts => $now }
+   } @$instances;
+
+   # If the file exists, read the instances in it, and if they're
+   # not one of the updated ones, save them with their original ts.
+   if ( -f $vc_file ) {
+      open my $fh, '<', $vc_file or die "Cannot read $vc_file: $OS_ERROR";
+      my $contents = do { local $/ = undef; <$fh> };
+      close $fh;
+
+      foreach my $line ( split("\n", ($contents || '')) ) {
+         my ($id, $ts) = split(',', $line);
+         if ( !exists $all_instances{$id} ) {
+            $all_instances{$id} = { ts => $ts };  # original ts, not updated
+         }
+      }
+   }
+
+   # Write back all instances, some with updated ts, others with their
+   # original ts.
    open my $fh, '>', $vc_file or die "Cannot write to $vc_file: $OS_ERROR";
-   foreach my $instance ( sort { $a->{id} cmp $b->{id} } @$instances ) {
+   foreach my $id ( sort keys %all_instances ) {
-      PTDEBUG && _d('Updated:', Dumper($instance));
+      PTDEBUG && _d('Updated:', $id, Dumper($all_instances{$id}));
-      print { $fh } $instance->{id} . ',' . $now . "\n";
+      print { $fh } $id . ',' . $all_instances{$id}->{ts} . "\n";
    }
    close $fh;
 
@@ -293,7 +316,7 @@ sub get_instance_id {
    }
    my $id = md5_hex($name);
 
-   PTDEBUG && _d('MySQL instance:', $id, $name, $dsn);
+   PTDEBUG && _d('MySQL instance:', $id, $name, Dumper($dsn));
 
    return $name, $id;
 }