A flash is not invisible as the code in the ECU is different. If BMW wanted to interrogate the ECU it would be VERY clear it has been tuned. Flashes have advantages but warranty invisibility is not one of them.
The other drawback of a flash is most can't be turned off so any test drive by a field tech would let the cat out of the bag. As Jon mentioned above the PBX can be removed for serious warranty work or just tuned off (100% stock programming).