Please post a piece of code that demonstrates the problem, including expected result and actual result. I could not reproduce the issue from your problem description.

use Data::Dumper;
%hoh = (
    'item1' =>  {
                       'key1' => '1',
                       'key2' => '1',
                       'key3' => '0'
                   },
    'item2' =>  {
                       'key1' => '0',
                       'key2' => '1'
                   }
);

print "Before delete:\n";
print Dumper \%hoh;

my $a = "item2";
delete $hoh{$a};

print "\n\nAfter delete:\n";
print Dumper \%hoh;
print "$a deleted!" if not exists $hoh{$a}; 
[download]

Before delete:
$VAR1 = {
          'item1' => {
                       'key2' => '1',
                       'key1' => '1',
                       'key3' => '0'
                     },
          'item2' => {
                       'key2' => '1',
                       'key1' => '0'
                     }
        };


After delete:
$VAR1 = {
          'item1' => {
                       'key2' => '1',
                       'key1' => '1',
                       'key3' => '0'
                     }
        };
item2 deleted!
[download]

That being said, you should abstain from using $a and $b as variables, as they have special meaning to the sort function.