Here's my TD1/warranty/tune write up that I post from time to time:
The warranty discussion is simple. If you flash the ECU and there are any powertrain-related warranty claims, those claims will be scrutinized under the lens that you modified/added more power - this will be referred to here in the VW online universe as "TD1". TD1 is a flag in the VAG system associated with your VIN that tells the dealer/warranty claim folks that your car has had it's ECU modified. It's automatically assigned when they scan the car a certain way and the dealer doesn't do it manually b/c "you are a scumbag tuner kid" or because "all dealers are out to get you" and I don’t care that your buddy’s friend’s sister’s brother works at a dealership and told her that he manually flags cars all day long – it’s BS. If VW think that this increase in power/modification caused or could have had anything to do with the failure, they will deny the claim. Simple and if I was the manufacturer, I'd do the same. VW can tell if you are/have been tuned if they have to do a scan to back the claim. If that is going to be a major financial issue for you, then don't tune it or go with a piggyback like the JB4 and be ready to remove it each and every time you go in to a dealer for service or warranty work - you also have to be ok with that in terms of the ethical considerations involved. I am tuned and have other hardware - I've had several warranty claims for some HVAC issues, recalls, and service campaigns - this is actually the crap that will be likely to fail vs. catastrophic engine/tranny failure everyone is so worried about. They were covered because they simply have zero do with the tune if they even looked for it for that type of claim (it's all about what VW requires the dealer to document to get paid for the warranty work/claim). If you did a poll here, most of the folks with off-the-shelf stage 1/2 tunes from the big players will have had no drama with their cars under the warranty period in terms of major failures that were denied because of the tune. Fact is, most cars never have major issues anyway. I've had 3 new cars in my life at 47, never once have I had more than nickle/dime crap fixed under warranty.