I know it's an old thread, but my Amulet Red bonnet has done exactly the same thing; the clear lacquer top coat started to come away in one small area as the result of a stone chip, and now there are dozens of patches where it's bubbled and started to peel. Moisture must get under the lacquer, causing it to lift I guess. The red paint coating itself is still perfectly intact underneath.
I thought I was being clever when I spotted an amulet red bonnet for sale on eBay and snapped it up. It arrived, but to my dissapointment had the early signs of the same thing happenning so now I have 2 bonnets with the same issue! Expect to see a patchy amulet red bonnet for sale on the forum some time soon!
As the car is now 10 years old I assume it's far too late to go back to Audi? Has anyone had any success with doing so?