This is a complicated issue, and is all down to the dealer, because if they are happy to submit a warranty claim to Audi, then I doubt Audi will question it most of the time, especially not going to the depths of finding out if the cars chipped or not.
But just bear in mind that it is their right to reject warranty if the car has been moddified and the failure can be related to the moddification.
You can also ask yourself if the dealer will actually notice if it's chipped or not.
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