I've never had a problem with any of my numerous tuned cars (both ECU and TCU) when flashing back to stock file before any trip to the dealership. Been doing that for over 10 years and 3 different Audis. But yea, as QShip mentioned...if you're worried, don't tune your car. If you have mods on your car and you end up coming in for something major, say a blown turbo or something, they're going to dig, and chances are even if you flashback they could find something that's enough for them to TD1 hammer you. Pay to play and all that fun.
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