They could technically write detection algorithms or something within the firmware/bios that tracks it and cannot be overriden, however, because I would guess something close to 98% of tunes that cause issues have very obvious signs (such as excessive rev limit) that it's not worth it to actually go out and spend to have this done. In addition, they KNOW these machines are destroyed by EPA and soon to come EU restrictions that they don't want to make it completely against warranty to tune the machines. Many dealers already help customers by installing BT/SLR etc.
z00, the laptop cannot power the ECU itself. It's writing (or reading) via the connection but it's not providing power (as far as how quick setup everything). He's using the device he posted to power the bike ECU using pos/neg connections regulated very carefully by the DC power source. I believe if you were really worried about it (which I am), you can get a portable power supply (that can be wall charged) and plug it in so that if the power goes out everything still stays up and doesn't brick your ECU. You can also for measure, plug in the laptop to the PPS just in case the battery on the laptop somehow in a million years fails and reverts back to it's charger for staying up (or you forget to charge the laptop and you keep it alive).
I am probably going to do some setup like that so that during a upcoming track day I can adjust the tune at the track and then next break between sessions flash the bike (taking the tank off and such as he mentions is pretty quick and simple after one or two times). It can be done within 40 minutes (including the flash) if you have everything setup and don't make mistakes while trying to reinstall the fairings because you are rushing. Maybe
@QuickSliver can verify this is correct and not a totally crazy and stupid thing to try.