1995 A6 2.0 Gearbox/'failsafe

I have a 1995 A6 2.0 a couple of days after driving through some water (not that deep) my Auto box has decided to go into what I believe you call failsafe mode.
Having read the old posts regarding similar problems and reading about a way to reset the electronics, could someone explain how to actually do this. Any help you could give would be greatly appreciated. I have tried disconnecting the battery, it was off the car for 5 days whilst re-charging, unfortunately this did not help.
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