No no, I mean eval to generate two near-identical subs at compile time — no AUTOLOAD funkiness or anything.

BEGIN {
    my $merge_code = <<'EOC';
    sub %s {
        my ($data) = @_;
        while ( $some_condition ) {
            # big loop, no embedded loops
            $count = $count1 %s $count2;
        }
    }
EOC

    eval sprintf $merge_code, merge => '+';
    eval sprintf $merge_code, unmerge => '-';
}
[download]

I think it's very clear what's going on here, and you still get the benefit of only maintaining a single copy of the code.