G'day TJCooper,

I got to this thread rather late. I'm unclear as to what happened with deletes and updates in your OP. Given what's there at the moment, this technique should do what you want:

#!/usr/bin/env perl -l

use strict;
use warnings;

use Inline::Files;

my %found;
/^>(.*)\Z/ and $found{$1} = 0 while <REFERENCE_FILE>;
my $re = '\b(' . join('|' => keys %found) . ')\b';

while (<SEARCH_FILE>) {
    ++$found{$1} while /$re/g;
}

print "$_ occurs: $found{$_}" for sort keys %found;

__REFERENCE_FILE__
>Apple
ignored blah blah blah
>Banana
ignored blah blah blah
>Grape
ignored blah blah blah
__SEARCH_FILE__
Apple Banana Avocado Orange
Grape Apple
Apple Banana Banana
[download]

Output:

Apple occurs: 3
Banana occurs: 3
Grape occurs: 1
[download]

I've used Inline::Files for demonstration purposes. You'll need to open your real files. I recommend you read the documentation and get into the habit of using the 3-argument form with lexical filehandles. Furthermore, if you're not going to write code to check your I/O, you should consider using the autodie pragma.