Hmmm, not sure on the warranty - I can't imagine Audi being too pleased about it but most mods are difficult to detect unless you go looking for them also some are more obvious than others.
I had the change made to my MMI system to allow the choice of default distance on the ACC by my dealer connecting my car to the computers at Audi AG on a 'After Sales Evening" they run every once in a while. There was no charge for doing this. I can only assume that as it's something that can be done by a dealer there would be no warranty problem if you do it yourself. The only difference is that mine is now on the Audi database as having been done.