(follow-up to Re: for loop error to handle identical keys at different nesting levels)

In case the two hashes are always structurally equivalent, you could use a "traversal-ID" ($id here) to make the keys unique by adding the ID to the keys. It's a bit of a hack because it relies on a number of assumptions, but hopefully, it helps...

For example, with a duplicate key 'a':

#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;

my %xhash = ('a' => {
                 'b' => {
                        'e' => 'E',
                        'c' => 'C',
                        'content' => 'B
'
                      },
                 'content' => 'A
',
                 'd' => 'D',
                 'a' => 'Foo'
               });

my %c_hash=('a' => {
                   'addval' => {
                                 'b' => {
                                          'addval' => {
                                                        'e' => {
                                                                 'addv
+al' => {},
                                                                 'repv
+al' => '5'
                                                               },
                                                        'c' => {
                                                                 'addv
+al' => {},
                                                                 'repv
+al' => '3'
                                                               }
                                                      },
                                          'repval' => '2'
                                        },
                                 'd' => {
                                          'addval' => {},
                                          'repval' => '4'
                                        },
                                 'a' => {
                                          'addval' => {},
                                          'repval' => '99'
                                        },
                               },
                   'repval' => '1'
                 });


my $id;
sub traverse {
    my ($hash, $callback, $mode, $start_id) = @_;
    return unless ref($hash) eq "HASH";
    $id = $start_id if defined $start_id;
    for my $key (sort keys %$hash) {
        my $val = $hash->{$key};
        if (ref($val) eq "HASH") {
            traverse($val, $callback, $mode);
            if ($mode eq "collect") {
                if (exists $val->{repval}) {
                    $id++;
                    $callback->("$key-$id", $val->{repval});
                }
            }
        }
        if ($mode eq "replace") {
            $id++ unless $key eq "content";
            $callback->("$key-$id", $val, $hash);
        }
    }
}

my %repl;  # lookup table: a => 1, etc.
traverse(\%c_hash,
         sub {
             my ($key, $val) = @_;
             $repl{$key} = $val;
         },
         "collect", 0
);
# print Dumper \%repl;  # debug

traverse(\%xhash,
         sub {
             my ($key, $val, $href) = @_;
             if (exists $repl{$key}) {
                 my $newkey = $repl{$key};
                 my ($oldkey) = split /-/, $key;
                 $href->{$newkey} = $val;
                 delete $href->{$oldkey};
             }
         },
         "replace", 0
);
print Dumper \%xhash;

__END__
$VAR1 = {
          '1' => {
                   '4' => 'D',
                   '99' => 'Foo',
                   'content' => 'A
',
                   '2' => {
                            '3' => 'C',
                            'content' => 'B
',
                            '5' => 'E'
                          }
                 }
        };
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