When u take your truck in to do warranty work you put your stock program back in? Cant they tell if you've had an aftermarket program on your vehicle?
Yes have it tuned stock when you bring it in. This isn't really to try to "fool" the dealer or anything, but more to protect your tune because if you bring it in and they do a pcm flash update or something along those lines they will overwrite your tune, then your tuner will be locked and useless.
As far as them knowing, the answer is "maybe". People claim they might be able to tell, but I have yet to hear of an actual case of this. Even if they can, I'd still tune my truck...