When the car gets remapped we have the option to zero the flash counter or revert it back the setting prior to there map. The remap wont show up on the dealers tools because the software code is the same as the std mapping, If the dealers could see the remap RSA key and checksumm then they could for deffo say it has been remapped. If they wanted to dig deep to void a warranty claim they could log the requested output values and compare with another car, or even test drive the car.
I tell all my customers the remap could void a warranty, I also tell my customers to be honest with there dealers and tell themthe car has been remapped, this way they will work with you, because at the end of the day they get paid to carry out warranty work.
Nick