Similar posts have been going around for a few months now. Not to mention that this is pretty old information. There is nothing new about their programing. Just another TSB. Of course, the Magnuson-Moss Warranty Act says that the dealer has to prove that the mod caused the damage. So in fact, GM is going to use a tune against you, assuming they can prove, or spend the time and money proving you had one. You might be interested in this thread on trailvoy.com: http://forums.trailvoy.com/showthread.php?t=38748

Pay special attention to what the tuner vendors have to say about the subject. Bottom line is that this is nothing to worry about. Most dealers will reflash before they take the time to track through the code looking for evidence of a hacked PCM.

 

The way I see a problem is like this: Suppose you cook a piston, burn it from running lean. Now the real reason is because your injector plugged partially, or something like that. The dealer pulls the head, sees heat damaged piston, notices you put a put a louder muffler on, so he checks for a tune. Low and behold, you are gonna be denied a warranty claim, because the "tune burned up your motor", when in fact an injector problem did.
Locally, a simular problem happend to a friend of mine. His college girls Cobalt, wouldn't start without the car jumping forward (Stick car) 34k miles. Obviously a clutch problem, had local dealer tow it in. The took it apart, normal clutch wear, noticed the front tires were pretty thin, decided the car had been abused(Heavy burnouts they said), and that the clutch had been toasted from that. Their mind was made up. I went and looked at car, noticed NO heat damage to pressure plate, no evidence of anything but normal dusty bellhousing, ALSO noticed leakage of fluid around clutch hydraulic throwout assembly. Humm, guess what? Bad clutch slave unit, leaking pressure off untill clutch wouldn't disengage. Dipshi@@ dealer insisited clutch was burned up, of course it was not disengaging, and not slipping which would have been the result of burned clutch. There was no pieces of rubber in the wheelwell from doing burnouts, tires were evenly worn side to side even though front wheel drive, and no limited slip, and it was a piddly 4 cyl to boot. It was from underinflated and not rotated tires of a girl away at school, not abuse of the drivetrain. They ended up paying $650 for a new clutch plate and flywheel, that WASN"T bad.
Long story, but I can see potiential problems for some who have a tune then have some other trouble with the car.