If you're swapping ECMs, one for the flash and the stock one, will your odometer reading and the ECM stored mileage reading get out of sync when you take the car into the dealer? Wouldn't this be a giveaway to the service tech that ECM mods are done to the car.
First the dealer would have to prove the computer swap is causing your warranty concern. But they really dont look for that. When I swapped mine, mielage stayed same on odometer. Thats what Tech will see, they usually arent digging around for stuff unless you blow your motor.
And there is way too much invloved to prove a mod was the cause of failure. If you use a reputable tuner like DC Performance, they will stand behind their work and if you ever had a problem, I bet they would help work things out with dealer, I really wouldnt worry about it.
And if your just going in for window prob, etc, they wont even care.