Welcome to the forum Antony :)
You'll find the members on here are a friendly and helpful bunch :)
Sorry to hear your having issues. I believe the water getting into the battery compartment and footwell is caused by the water channels being blocked by debris, leaves, dirt etc. Once the water starts seeping into the cabin in interacts with the electrical systems which run behind the dash. The a6 has a fuse box on either side of the dash. The ends of the dash pull off to reveal the fuses etc. It then causes havok with the systems.
My best advice is to get an auto electrician on the case but I suspect it could have affected the module for the central locking. Sorry I can't help more.
Cheers
Steve