( for reference: for loop error )

As every value in your %xhash structure is now wrapped in an array (including its hashes), you'd need to adapt the traverse() routine to dive into those arrays. For example:

sub traverse {
    my ($hash, $callback, $mode) = @_;
    traverse($hash->[0], $callback, $mode) if ref($hash) eq "ARRAY";  
+  # <---
    return unless ref($hash) eq "HASH";
    for my $key (keys %$hash) {
        my $val = $hash->{$key};
        if (ref($val)) {
            traverse($val, $callback, $mode);
            if ($mode eq "collect") {
                if (exists $val->{repval}) {
                    $callback->($key, $val->{repval});
                }
            }
        }
        if ($mode eq "replace") {
            $callback->($key, $val, $hash);
        }
    }
}
[download]

Output:

$VAR1 = {
          '1' => [
                   {
                     '4' => [
                              'D'
                            ],
                     'content' => [
                                    'A'
                                  ],
                     '2' => [
                              {
                                '3' => [
                                         'C'
                                       ],
                                'content' => [
                                               'B'
                                             ],
                                '5' => [
                                         'E',
                                         'V'
                                       ]
                              }
                            ]
                   }
                 ]
        };
[download]

(Also, as "$hash" has now become a misnomer, I'd change it to something more generic, like $node, or some such... but I left that for you to do :)