Here's an approach that initializes a hash of output tokens, prepopulated with marker text for new additions. The output data is overridden for existing entries, and a sorted list is appended to the specified output file (open with '>' instead of '>>' if you don't want this). Note that it isn't fully compatible with the delete code I posted earlier, since that code didn't take comments into account.

#!/usr/local/bin/perl
use strict;
use warnings;

if (@ARGV != 3) {
    print "Usage: $0 <pattern file> <input file> <output file>\n";
    exit;
}

my ($pattern_filename, $source_filename, $dest_filename) = @ARGV;

open my $pattern_fh, '<', $pattern_filename or die "Failed to open $pa
+ttern_filename: $!";
my %output_tokens = ();
while (my $line = <$pattern_fh>) {
    chomp $line;
    $output_tokens{$line} = "$line # Added by script";
}

print "Expected tokens: ", join(', ', keys %output_tokens), "\n";

open my $infile, "<",  $source_filename or die "Failed to open $source
+_filename: $!";
open my $outfile,">>", $dest_filename   or die "Failed to open $dest_f
+ilename: $!";

while(my $line = <$infile>) {
    chomp $line;
    $output_tokens{$line} = $line;
}
for my $token (sort keys %output_tokens) {
    print $output_tokens{$token}, "\n";
}

close($infile);
close($outfile);
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