I had a 2008 Jetta 2.0 TSI 6DSG from new and had it APR tuned before the first year was up... I serviced it with an Independent VW/Audi specialist and only took it to the dealer for warranty work. I was experiencing DSG issues and took it in under warranty to get checked. It went in a few times, each time with them trying different things with the DSG and eventually they replaced the DSG under warranty. Not once did they question me on where it was serviced or mention the ECU changes via APR tune. Though one mechanic did comment to me when handing me the keys that the "car goes pretty good!" with a big smile..
So I never had any problems with VW over the car being modified even though they probably could've easily blamed whatever was wrong the with DSG on the modification.
1974 1300 Beetle, 1997 Golf GL, 2003 New Beetle Cabrio, 2014 Audi A4 quattro
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