A tech can tell if you have tuned your raptor, even if you return it to stock. Ford got pretty smart with all of their vehicles in the last few years, and just so you know, if your aftermarket tune is detected, it will void your entire power train warranty and even SOME electrical components as well.
Ford dealers will typical have techs that while they make the most stupid mistakes in the world that even a typical mechanic would never screw up, They are trained on detecting tunes over any other aspect of their jobs. Why? If you break it and they can prove you had a tune, they stand to make a tremendous amount of additional money from that. Ford pays a set amount for warranty work, it is paperwork intensive, and dealers consider it a heavy burden of their labor force.
This is the short answer believe it or not, and it can get extremely unpleasant for the owner, even if they are on the right side of the issue.
Beware- if you tune, don't admit it online, and don't ever take your truck in for any service with your tuner in the vehicle.
I have heard that returning your truck to stock tune, and THEN disconnect battery for hard reset, and run truck for a couple hundred miles as your truck's computer is attuitive meaning it learns and adjusts certain settings and ratios for tunes that leave a red flag if you don't do all above steps. Even at that, your PCM keeps a reflash count, so they will know if you change your tune back and forth a lot, another red flag. If its just one or two times, they cannot prove it was tuning by the customer unless they have a documented flash count from a previous servi e visit.
I have had MUCH experience in this and know one of the premier tuners that works for Ford. I am not trying to discourage, just give the real information they use against you.