You can use Data::Dumper to assure yourself that delete is working.

use Data::Dumper;

my $var = { '1234-567' => { 'key1' => 'stuff' ,
                         'key2' => 'stuff',
                       },
         '1234-997' => { 'key1' => 'stuff' ,
                         'key2' => 'stuff',
                       }
       };

print Dumper($var);
delete $var->{'1234-997'};
print Dumper($var);
[download]

produces

$VAR1 = {
          '1234-567' => {
                          'key2' => 'stuff',
                          'key1' => 'stuff'
                        },
          '1234-997' => {
                          'key2' => 'stuff',
                          'key1' => 'stuff'
                        }
        };
$VAR1 = {
          '1234-567' => {
                          'key2' => 'stuff',
                          'key1' => 'stuff'
                        }
        };
[download]

You're getting bitten by the fact if $var->{a} doesn't exists, then tests on $var->{a}->{b} will autovivify $var->{a} (though the same test on $var->{a} wouldn't.)

my $var = {};
print if exists $var->{a};
print Dumper($var);

print if exists $var->{a}->{b};
print Dumper($var);
[download]

produces

$VAR1 = {};
$VAR1 = {
          'a' => {}
        };
[download]