If you got merit for a post, you won't lose it, and it doesn't matter if the post or the thread in which its in gets deleted. That's one of the things I like about the merit system--it's permanent. You can lose activity and posts, but you cannot lose merits once received.
I really like the idea of merits are permanent once you earned it, but the farmers use this method to cover their farming act and i guess it is hard to track it back for normal member, unless the tracker is moderator or administrator i guess, but once again, there are not many moderators in this forum to prove some merit farming act.