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

for my $k ( keys %harry ) {
   my $a1 = $harry{$k};
...
   @$a1 = map $a1->[$_], grep !$delete_a1{$_}, 0..$#$a1;
   @$a2 = map $a2->[$_], grep !$delete_a2{$_}, 0..$#$a2;
}

for my $k ( keys %harry ) {
   my $a1 = $harry{$k};
...
   @$a1 = map $a1->[$_], grep !$delete_a1{$_}, 0..$#$a1;
   @$a2 = map $a2->[$_], grep !$delete_a2{$_}, 0..$#$a2;
}

for my $k ( keys %harry ) {
   my $a1 = $harry{$k};
...
   @$a1 = grep $seen{$_}>1, @$a1;
   @$a2 = grep $seen{$_}>1, @$a2;
}