Unfortunately, a lack of evidence cannot be guaranteed on late-model F-150s. I believe the dealership can see when it's been flashed even if you've reset it back to factory programming. Regardless, I've never wanted to risk it during the warranty period. Seems to me that they're always looking for excuses to void warranty repair as it is...
2011 F150 5.0 Supercrew 4X4 Off Road
U.S. Air Force Retired.