My 3.2 has never done this and I have not heard anything about it.
I would have an independent shop replace the inlet manifold with a used part. I would also have them confirm that the pneumatic control ( and system) is working correctly also.
This problem has a smell to it, in that, Audi noted the history fault codes but could not replicate the fault on site. The diagnosis is based on past fault codes and with a change the whole thing approach. I would be asking on forums for a good Audi independent in your local area, take it there for a second opinion.