I don't seem to recall any issues from the 3.0T. However, I would be weary of a car that was in an accident. How bad was the accident?
Something you should know about CarFax... If a car is in an accident, you will never be sure how BAD the accident was. If it says "Major" accident, the car you're looking at might have only been scratched, but if an air bag goes off in another vehicle involved in the same accident, it will say that it was bad. If the car you're looking at was badly damaged, but no air bags went off in the crash, it will say, "Minor."
Although I never like to offer information about wasting a dealer's time, I would ask your sales consultant if you can drive a 2012 A6 3.0T, and then the 2009 model, to ensure that the engine pulls and does everything the same. No major differences between the two model year engines. I would assume that there is an additional warranty on an engine replacement, but I've never run into that. Purchasing a CPO car can be a good value, as long as you don't drive 30k miles per year. The warranty is the same as a factory warranty, but longer.
Just be sure the engine doesn't fall out of the bay, and take it to a reputable German mechanic to be checked out. Good luck!