If it is a gearbox swap, I read somewhere recently that VAG Can Pro was used to read the flash from the original TCU and then this binary was reflashed to the new/used gearbox for it to work. So if there are software problems with used boxes in different cars there are solutions. 
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Matt
2004 A8 3.7q, 1998 A4 2.8q, 1994 Coupe 2.8q SORN,
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