I tried it like this:

#!/usr/bin/perl

use strict;
use warnings;
use Storable qw(retrieve store retrieve_fd store_fd);
use Fcntl qw( :flock );

my $file = '/tmp/storable_test';
my (%data) = ( item => 'Here I am' );
store(\%data, $file );

open my $fh, '+<', $file;
flock $fh, LOCK_EX();

my $data = retrieve_fd( \*$fh );
print 'item: ', $data->{'item'}, $/;

delete $data{'item'};

print 'gone (error as expected): ', $$data{'item'}, $/;

store_fd( $data, \*$fh );
close $fh;

my $check_data = retrieve($file);
print 'why is this here? ', $$check_data{'item'}, $/;
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It returned this:

item: Here I am
gone (error as expected): Here I am
why is this here? Here I am
[download]