for my $k ( keys %harry ) {
   my $a1 = $harry{$k};
   my $a2 = $harry{$phash{$k}};

   for (my $i1 = @$a1; $i1-- >= 0; ) {
   for (my $i2 = @$a2; $i2-- >= 0; ) {
      next if $a1->[$i] ne $a2->[$i2];
      splice( @$a1, $i1, 1 );
      splice( @$a2, $i2, 1 );
      ...
   }
}