I am not quite sure I understood your question. Try this out..I think this kludge might be what you are looking for.

use strict;
my %hash1 = (
    A => 5,
    B => 7,
    C => 2,
    D => 8,
);
my %hash2 = (
    1234 => "A,C",
    4567 => "A,B,D",
    5678 => "C",
);

my %hash3;

foreach my $key2 ( keys %hash2 )
{
    my %temphash = %hash1;
    foreach ( split /,/, $hash2{$key2} )
    {
        delete $temphash{$_};
        $hash3{$key2}= join ',', sort keys %temphash;
    }
}

foreach my $key ( keys %hash3 )
{
    print "$key : $hash3{$key}\n";
}
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