In most cars you can tell when the ECU has been flashed because it erases the key cycles, this is how most Dealers find out. This will happen when flash programmers are used hyper tech, Preditor and such. Programs like EFI live won't be picked up at a Dealership because it uses the Factory style inscription but if the ECU is sent out because of warranty concerns it can be picked up also but it is much harder to find and won't accept being flashed over.