I don't agree Phil. I think you should push Skoda. Then decide if you want them to do it, or if it'll be more cost effective to use a good indy.
If you look at what happened to me, it would have cost me £250. Having had the car remapped (after the warranty expired I might add) was my downfall, as Skoda UK used it as a get-out card (which of course it is).
So long as you've not had anything done that would void the warranty, if I were you, I'd be pushing Skoda. I take John's point, turbo's let go, sh 1t happens. I had a B5 Passat that was at 275k and on it's original turbo when I sold it. There are plenty of tales of turbo's lasting a very long time, but there are also those of us who've experience the opposite from time to time. Googling IS20 Turbo longevity/lifespan brings up some very interesting results.
Best o'luck with getting it fixed 👍
Gaz