Isn't this pretty much exactly what we've already had in Hash handling error?

The only difference I can spot is that the value associated with 'e' / 5 in that node had been ['E','V'] instead of ['E'].  The solution I suggested should equally be applicable.

Update: complete code (as I understand your task) — just in case:

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

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

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'
                                        }
                               },
                   'repval' => '1'
                 });

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);
        }
    }
}

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

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

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

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