I had 2 turbo's replaced on my Uni stage 2 Gen3 GLI. All under warranty. VWoA tried proving there was a tune because my catless downpipe would not throw a code on the stock tune. They had my car for a month. No proof found. Got it fixed. Even smelling like race gas.
A failed 2nd o2 sensor did not show failed...but was causing crazy hpfp pressure fluctuations as well. Just unplugging the 2nd O2 will cause a staling and over fueling issues stock or tuned.
Its an order of operations. Make sure your ecu is up to date with the latest oem software. Get a tune. Make sure you flash back to the exact stock revision on ANY dealer visit. APR, Uni, ED, Revo, and Gaic might all have different ways of flashing.