You want something like Tie::File. This would allow you to edit the master file in place (unless that's a problem) Also it seems like you only need an array, as there is no association to be made (ie all it seems you are populating is that a hash key hashes to one when it needs to be deleted. You would be better off doing something like this

open(DELETE,$file) or die "$!";

my @delete = <DELETE>;

chomp for(@delete);

close(DELETE);

open(MASTER,$file) or die "$!";
open(OUTPUT,$file) or die "$!";

while(<MASTER>)
{
   my $zip = substr($_, 3, 9);

   if(!deletable(\$zip,\@delete))
   {    
      print OUTPUT, $zip;
   }
}
close(OUTPUT);
close(MATSER);

sub deletable
{
   my ($item,$list) = @_;  

   my $rv = 0;

   foreach(@{$item})
   {
     if($$item eq $_)
     {
        $rv = 1;
        last;
     }
   }
 
  return $rv;
}
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that's untested but its how i see it working best...Tie::File is a good option.. but if you're wanting to keep the same format.. this should work. This is all assuming that your delete file isn't ginormous.