The best thing i could come up with was something that identified which keys have duplicate values but i don't know how to delete all but 1.

Can you share your code?

Edit - Here's one option:

use strict;
use warnings;
use Array::Compare;
use Data::Dumper;

my %hash = (
    'a' => [ '1', '2' ],
    'b' => [ '2', '3' ],
    'c' => [ '1', '2' ]
);

my $comp = Array::Compare->new;

for my $key1 ( keys %hash ) {
    for my $key2 ( keys %hash ) {
        next if $key1 eq $key2 or !$hash{$key1};
        delete $hash{$key2}
          if $comp->compare( \@{ $hash{$key1} }, \@{ $hash{$key2} } );
    }
}

print Dumper \%hash;
[download]

Output:

$VAR1 = {
          'c' => [
                   '1',
                   '2'
                 ],
          'b' => [
                   '2',
                   '3'
                 ]
        };
[download]

The or !$hash{$key1} notation avoids autovivification in cases where the key no longer exists.