You'll be ok. Remember, the dealer wants to repair the vehicle. Service department and parts department make $$$ from Audi of America through warranty claims. It's when the vehicle has been red flagged for a flash (td1) that warranty claims get kicked back to a dealer, which they eat the cost of repair and reimburse Audi of America for a repair that shouldn't have been done.
It's a big grey area on certain things, with many variables. When the "mod" is part of the system of where the malfunction/defective part occurs, that's when a dealer is reluctant to want to make repairs because the chance of a warranty claim getting kicked back to them.
Without going into detail, there's a big process after repairs are made, dealership warranty clerk submits claims through a system, goes to a specific department within VWGoA, claims reviewed, accepted or kicked back, sent over to AG for review/payment.... can be kicked back at this levels well. Also the "defective" parts dealer return can be tested, if found to be in working condition, claim gets kicked back.
Just thought I'd give you better insight on how things work without confusing you too much.
My guess you have OB5 7-speed gearbox, without knowing the faults, I'll say you'll either need a flash, updated harness only, mechatronic unit with updated harness or transmission. Which the dealer is hoping transmission.
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