I’d strongly advise you to have the car flashed back to stock before taking the car into the dealer. The VW diagnostic system can detect any changes to the software from standard. This is then updated by the VW central system and a record created that non-standard software was found on the vehicle. That could impact any future warranty claim.
As a Revo dealer, I accept that customer cars will need to be flashed multiple times to keep the warranty intact. Generally I make no charge to my customers for this, as it’s good customer service. But I can’t speak for other dealers.
Hope this helps.