Personally, if you can’t fix the item to work for the user, then I’d give them a refund. It’s not your fault persay, but they are still stuck with a useless item since they can’t get it work. You’ve verified that the user can’t get it to work too, so you know they aren’t pulling your leg.
Yes the timing sucks. Waiting this long after reporting an issue is annoying.
I work a lot with CodeIgniter- did you know you don’t have to use mod_rewrite rules in order to get the application to work? You can simple just use the $config[‘index_page’] = ‘index.php’; rule in your config which can be used as an alternative.