use strict;
use warnings;

use Data::Dumper;

my $W={
    'A' => {
        'L' => {
            'D'=>99,
            'X'=>99,
              },
        'C' =>{
            'E'=>99
             },
          }, 
    'X' => {
        'Q'=>{
            'O'=>99,
            },
        'T'=>{
            'U'=>99,
            },
          }, 
    };

remove($W, 2);
print Dumper($W);

sub remove {
    my ($p, $d) = @_;
    if ($d-- > 1) {
        remove($_, ($d)) for values %$p; # Had second decrement here
    }
    else {
        my %newhash;
        for (values %$p) {
            @newhash{keys %$_} = values %$_;
        }
        $_[0] = \%newhash;
    } 
}