I'd say that it certainly must a result of running a K03 map with a K04 turbo, and booting it whilst you're at it.
Given the recent turbo upgrade,I do sympathise and i feel that it must have been really hard not to give it some beans, and I genuinely hope that the £ damage caused is not too great.
Without wanting to knock down the mechanic you're using, is he knowledgeable on the 2.0TFSI? If not, it really may be better to see a specialist such as JKM, R-Tech, Jabba etc, and get everything sorted in one hit.