Update: Yes, there's something going on here -- my example below has to do with a one-level hash, whereas the original is about a two-level hash. Nothing to see here. This is not the Perl code you're looking for. You can go about your business.

There must be something else going on here. Here's a simpler example that shows that I end up with fewer keys than I started with -- using just a one-dimensional hash. Code:

#!/usr/bin/perl

use warnings;
use strict;

use Data::Dumper;

{
        my %hash = ( 1 => 5, 3 => 12, 7 => 19, 9 => 44 );
        print 'At '
          . __LINE__
          . ' there are '
          . ( scalar keys %hash )
          . " keys: ";
        print Dumper(\%hash);

        my %hash2 = ( 1 => 5, 9 => 22 );
        print "This should delete one of the keys, using this hash ..\
+n";
        print Dumper ( \%hash2 );

        foreach my $key ( keys %hash2 ) { 

                if ( exists $hash{ $key } ) { 

                        $hash{ $key } -= $hash2{ $key };
                        if ( $hash{ $key } <= 0 ) { 

                                delete $hash{ $key };
                        }
                }
        }
        print 'At '
          . __LINE__
          . ' there are '
          . ( scalar keys %hash )
          . " keys: ";
        print Dumper(\%hash);
}
[download]

.. and the result:

tab@music4:~/Pianoforte/Development/Perlmonks/11113721 $ perl hashkeys
+.pl
At 11 there are 4 keys: $VAR1 = {
          '9' => 44,
          '1' => 5,
          '3' => 12,
          '7' => 19
        };
This should delete one of the keys, using this hash ..
$VAR1 = {
          '1' => 5,
          '9' => 22
        };
At 33 there are 3 keys: $VAR1 = {
          '9' => 22,
          '3' => 12,
          '7' => 19
        };
tab@music4:~/Pianoforte/Development/Perlmonks/11113721 $
[download]

I set the example up so that one of the keys would end up with zero (and get deleted), and another would be reduced, but not to zero. I started up with four keys, and finished with three.

Check your code -- I'm guessing you're missing something.

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