the modification has to have caused the failure. putting a tune on your car doesn't void warranty for seatbelts, airbags, wheels, interior trim bits, etc. Same for recalls and TSBs. if you put a tune on your car and blow a turbo, that's on you. They can tell, since every time you flash the car, it increments the counter referenced above, but if it isn't for what they're looking to repair, they can't deny coverage.