The result is something like $VAR1->{'1'}{'test2'}.
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That's just due to the way Data::Dumper has to represent the data. In order to allow for the feature to be able to recreate the original data structure by eval-ing Data::Dumper's output, it cannot repeatedly expand substructures, because in that case you'd get a new instance of the structure (hash, array,...), instead of a reference to the existing structure.

Try print Dumper $ref_2a, $ref_2b; in VERSION 2, and you'll see that it now also shows

$VAR2 = {
          '2' => {
                   'test1' => {
                                '1' => $VAR1->{'1'}{'test1'},
                                ...
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instead of the expanded style you got before

$VAR1 = {
          '2' => {
                   'test1' => {
                                '1' => {
                                         'key2' => '2',
                                         'key1' => '1',
                                         'key3' => '3'
                                       },
                                ...
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That's because now it has already encountered (and displayed (or created upon eval-ing ...)) the structure referenced by $VAR1->{'1'}{'test1'}.

Sounds like you want use Storable qw(dclone), which performs a "deep clone" of nested data structures:

use Storable qw(dclone);
foreach my $b1 (keys %{$ref_1->{'1'}}) {
    if(exists $ref_1->{'2'}->{$b1}) {
        $ref_1->{'2'}->{$b1}->{'1'} = dclone $ref_1->{'1'}->{$b1};
    }
}
print Dumper $ref_1;
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Side note: In Perl, pointer syntax (->) is optional after the first one; that is, $ref_1->{1}->{test1}->{1} is equivalent to $ref_1->{1}{test1}{1}.

          '2' => {
                   'test1' => {
                                '1' => $VAR1->{'1'}{'test1'},
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try this

use Data::Dumper;

# VERSION 1
my $ref_1;

$ref_1->{'1'}->{'test1'}->{'key1'} = '1';
$ref_1->{'1'}->{'test1'}->{'key2'} = '2';
$ref_1->{'1'}->{'test1'}->{'key3'} = '3';
$ref_1->{'1'}->{'test2'}->{'key1'} = '4';
$ref_1->{'1'}->{'test2'}->{'key2'} = '5';
$ref_1->{'1'}->{'test2'}->{'key3'} = '6';

$ref_1->{'2'}->{'test1'}->{'key1'} = '1';
$ref_1->{'2'}->{'test1'}->{'key2'} = '2';
$ref_1->{'2'}->{'test1'}->{'key3'} = '3';
$ref_1->{'2'}->{'test2'}->{'key1'} = '4';
$ref_1->{'2'}->{'test2'}->{'key2'} = '5';
$ref_1->{'2'}->{'test2'}->{'key3'} = '6';

foreach my $b1 (keys %{$ref_1->{'1'}}) {
    if(exists $ref_1->{'2'}->{$b1}) {
        $ref_1->{'2'}->{$b1}->{'1'} = $ref_1->{'1'}->{$b1};
    }
}

$Data::Dumper::Deepcopy=1;
print Dumper $ref_1;
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