The best thing to do is get a tuned ecu that has an image of the original tune(better tuners can do that) or swap it out each time you think the car may have to be scanned.
I'll restate this a tad:
The ONLY thing to do is get a SECOND ecu that has the tune AND swap it out EVERY time you take the car to the dealer.
... Remember if there are open TSB's, etc (which show up when the RO is created) it gets hooked up and a tuned ECU will automatically VOID THE WARRANTY! The ECU remembers that it has been reprogrammed even after you 'untune' it and this also automatically VOIDS THE WARRANTY! Ask any Camaro guy. The only way around it is to have 2.
But I don't know for sure what other parameters the ECU 'remembers' ... so it may actually be deducible by mileage, total engine hours, cycles, and/or a myriad of other things that the ECU was swapped!
Remember this is Global Architecture 2 and big brother is watching!