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]

mam this output only i have from your code see the error inner keys are not replaced

_OUTPUT_
$VAR1 = {
          '1' => [
                   {
                     'b' => [
                            {
                              'e' => [
                                     'E',
                                     'G'
                                   ],
                              'c' => [
                                     'C'
                                   ],
                              'content' => 'B
'
                            }
                          ],
                     'content' => 'A
',
                     'd' => [
                            {
                              'content' => 'D
',
                              'x' => [
                                     'C'
                                   ],
                              'z' => [
                                     'E',
                                     'G'
                                   ]
                            }
                          ]
                   }
                 ]
        };
_INPUT_
my %xhash=('a' => [
                 {
                   'b' => [
                          {
                            'e' => [
                                   'E',
                                   'G'
                                 ],
                            'c' => [
                                   'C'
                                 ],
                            'content' => 'B
'
                          }
                        ],
                   'content' => 'A
',
                   'd' => [
                          {
                            'content' => 'D
',
                            'x' => [
                                   'C'
                                 ],
                            'z' => [
                                   'E',
                                   'G'
                                 ]
                          }
                        ]
                 }
               ]);
my %c_hash=('a' => {
                   'addval' => {
                                 'b' => {
                                          'addval' => {
                                                        'e' => {
                                                                 'addv
+al' => {},
                                                                 'repv
+al' => '5'
                                                               },
                                                        'c' => {
                                                                 'addv
+al' => {},
                                                                 'repv
+al' => '3'
                                                               }
                                                      },
                                          'repval' => '2'
                                        },
                                 'd' => {
                                          'addval' => {
                                                        'x' => {
                                                                 'addv
+al' => {},
                                                                 'repv
+al' => '10'
                                                               },
                                                        'z' => {
                                                                 'addv
+al' => {},
                                                                 'repv
+al' => '11'
                                                               }
                                                      },
                                          'repval' => '4'
                                        }
                               },
                   'repval' => '1'
                 });
[download]

You must be using code different from the one I posted.  When I use your input %xhash and %c_hash in the exact above code, I get

$VAR1 = {
          '1' => [
                   {
                     '4' => [
                              {
                                '11' => [
                                          'E',
                                          'G'
                                        ],
                                'content' => 'D
',
                                '10' => [
                                          'C'
                                        ]
                              }
                            ],
                     'content' => 'A
',
                     '2' => [
                              {
                                '3' => [
                                         'C'
                                       ],
                                'content' => 'B
',
                                '5' => [
                                         'E',
                                         'G'
                                       ]
                              }
                            ]
                   }
                 ]
        };
[download]

As far as I can tell the only difference between the current output of your code and the output you indicate that you want is the hash references are nested in array references. That being the case the following version of the call back sub does the trick:

    sub {
        my ($key, $val, $href) = @_;
        if (exists $repl{$key}) {
            my $newkey = $repl{$key};

            $val = [$val] if ref ($val) eq "HASH";
            $href->{$newkey} = $val;
            delete $href->{$key};
        }
[download]

Note the $val = [$val] ... line.

I would recommend you read up on how Perl's array and hash structures work and on how to populate as well as iterate over them. Check here for a good start - perldsc

It also helps to initially draw your data structures on paper.

satzbu, please mark your updates , thank you. How do I change/delete my post?

You're running code, getting an answer, posting it here, and asking for help.

This is not, as they say, a sustainable development model.

Do you have tests? Are you using a source code management tool? I know - you don't have time. But consider: your development cycle is now at the mercy of folks deciding to help. You need to do more to help yourself.

Take one example of your input and expected output, and write a test. Use Test::Deep to check the differences between the data structure you're getting and the one you want. Start using the debugger to step through the manipulations of the data structure to check that each step is doing what you want, or to find where it's not.

You don't have to use something complicated to start doing source control. Use RCS. You don't have to set up a repository, and there are very few commands. Learn SVN or Mercurial or git some other time.

The only person who can really invest in this code is you, and you need to treat yourself right and give yourself the tools you need to fix this. I realize that you're probably under pressure to get this done, but your current working method will not do it.