I don't want you to have the run-around I was given by an ignorant customs lady. I didn't know VAT refund procedures had changed as I don't travel to Munich that often these days. Iwent to the place I knew off and got sent to the new place to get told that I need to check in first. Back all the way to to check-in, and back to customs....
In the past every terminal had a customs post where you could get your invoices stamped.
Bills for VAT refund can now get stamped only in a specially assigned customs office (and it seems to be the only such office) in Terminal C?
You have to check-in your luggage first, tell the airline clerk that you want your case back for customs inspection, then you go to the customs station in Terminal C?, get the stamp, show your items if requested. Customs will then send your case directly down the hatch.
Sorry, I can't remember if it was Terminal C but it must be as I checked in in B and it was way down the terminal.