The amount of misinformation on this topic is unreal. Nothing "voids" your warranty. Adding a flash tune (APR etc.) to your car *may* cause issues with powertrain warranty claims. VW gets to make that call, not your dealer, regardless of what they tell you. APR Plus is a third-party warranty that will cover what VW won't (b/c you have tuned your car), it obviously has stipulations. Read the warranty 101 post that is sticky'd on this page. Example - I have a tune and had no issue getting an HVAC issue covered under the warranty. If I blow my DSG, that may not get covered. You can not modify your car and expect VW to cover everything, period. If you can't afford to deal with a costly repair warranty claim that will be denied, don't tune your car.
Yeah.... uhhh, no. There are several things that can "void" your entire warranty (salvage, water damage, heavily modded to the point that virtually every system is touched, odometer fraud etc.) but you're right that the "tune" isn't one of them.
That said, the popular conception that piggyback tunes are 100% safe is inherently wrong even if there
is little evidence on the forums.
We know that VW can and will flag a car that has been flash tuned with a TD1 flag. This flag is place by the computers in Germany following a scan and is not disclosed until a warranty claim is submitted and declined.
There is another, more little known flag, that is placed when a dealer finds evidence of a piggyback tune. This TD4 flag has the same end effect as a TD1 with the exception that there can be little or no evidence to support the flag.
The ECU tracks the number of times it has been altered, so a flash will always leave a trace behind and the TD1 can always be supported. The TD4 relies on a report from a dealer/mechanic and may rely on seeing an actual piggyback installed
or evidence of a prior installation. I don't believe that there is a requirement to provide photos, so it is somewhat subjective.
There are numerous reports of TD1 warranty service denials, but very few TD4 denials, but the mere fact that it exists and VW has asked dealers to report piggybacks is sufficient to say that a piggyback is not 100% safe.
The APR warranty has enough loopholes to drive a semi through, so one can't really assume that is 100% sure either. Read the provisions of the warranty and you may be surprised.
If you mod, you need to mentally and financially prepared to pay for whatever the mod breaks - or what the dealer says the mod broke. You can then be pleasantly surprised when VW does cover the failure.