If I understand things right... If you have returned your truck to the stock tune before taking it in to the dealer, the dealer would have to be actively looking for evidence of a tuner in order to tell if you had used one or not. They probably won't be looking to see if you have used a tuner unless there is some sort of problem with the truck that they suspect was caused by a tuner. Under most circumstances, you'll probably be fine as long as you return the truck to the stock tune prior to taking it to the dealer for service.
*note all of the "probably"s in there- I'm not disagreeing with icOVERu, just offering an opinion on the probability of running in to an issue