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 );
      ...
   }
}

##</code><code>##

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

   my %delete_a1;
   my %delete_a2;

   OUTER:
   for $i1 ( 0 .. $#$a1 ) {
     #next if $delete_a1{$i1};  # Never true.

      for $i2 ( 0 .. $#$a2 ) {
         next if $delete_a2{$i2};
         next if $a1->[$i1] ne $a2->[$i2];

         $delete_a1{$i1} = 1;
         $delete_a2{$i2} = 1;
         next OUTER;
      }
   }

   @$a1 = map $a1->[$_], grep !$delete_a1{$_}, 0..$#$a1;
   @$a2 = map $a2->[$_], grep !$delete_a2{$_}, 0..$#$a2;
}

##</code><code>##

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

   my %seen;
   for ( @$a1 ) {
      push @{ $h1{$a1} }, $_;
   }

   my %delete_a1;
   my %delete_a2;
   for ( 0..$#$a2 } ) {
      my $seen = $seen{ $a2->[$_] };
      if ( $seen && @$seen ) {
         $delete_a1{$_} = shift(@$seen);
         $delete_a2{$_} = 1;
      }
   }   

   @$a1 = map $a1->[$_], grep !$delete_a1{$_}, 0..$#$a1;
   @$a2 = map $a2->[$_], grep !$delete_a2{$_}, 0..$#$a2;
}

##</code><code>##

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

   my %seen;
   ++$seen{$_} for @$a1, @$a2;

   @$a1 = grep $seen{$_}>1, @$a1;
   @$a2 = grep $seen{$_}>1, @$a2;
}