Most tuners replace the stock programing with an altered tune. You can return the stock tune but it isn't undetectable. If they examine the data on the ECU they can see that the stock data was reflashed back to the ECU. A standard diagnostic tool used for most service work to read codes isn't going to uncover it, but it can be found if they go in depth. Unless there is a reason to look (like the example provided of a new engine failure or you have been bragging to the service manager about your HP increases, etc.), it shouldn't be an issue. Normal services won't raise any suspicion. I've had a tune on my 2002 Silverado 2500HD since it was a week old and have had service work done, including replacing faulty injectors under warranty without even removing the tune. That being said, there is always a risk. Under law, they can't void your warranty unless the tuner actually caused the problem, but it is on you to prove that it didn't cause the issue. This can be problematic and costly. A good relationship with you service manager is always a good idea.
