Some reckon tuning boxes can be detected by looking at the car's logs (as said above) which would then be seen as anomalies if you'd removed the box prior to servicing - but they'd have to go looking for them. They'd also have to put together a strong argument together to pin these 'anomalies' on to a tuning box, as far as I can see at this stage it's your word against theirs unless they go to your house and turn it out to find your tuning box ....
Perhaps the answer here is how much logged data the car stores, I.e. How far back? Once you find that out just remove the box prior to service or warranty work by that amount of days or whatever it is and drive it around in stock form.
The only real issue you'll potentially get is clutch slip from what I've read up on, but many tuning box users seem to not have had any issues themselves. If you don't do loads of fast launches all the time you'll probably be alright. Even saying that, Audi know the clutches in these cars are a weak point as so many have been done on warranty already.