Gudoldtom

Hi my A6 Allroad has been stood for six months as I have been working away. When I opened the door manually as I disconnected the battery, the passenger side footwell and rear passenger side footwell was totally flooded. I opened the bonnet & the battery compartment above the engine is also flooded. It looks like when it has been raining the water has been flowing down the windscreen into the engine compartment where the battery is located & once it has filled up with water it then has leaked into the vehicle itself. I have managed to bail out the water & reconnect the battery & it starts up ok. The problem I am now having is with the central locking, windows & remote. When I first connected the battery I started the car but none of the doors would open though the fob or from inside the car using the central locking button or physically from the door handles. I left it for a couple of days & when I had reconnected the battery today, I went back inside & when I came back out the indicators all round the car were on, not blink but a solid glow. I opened the driver lock with the key & all the doors unlocked but 3 of the windows (2 front, 1 rear) have opened half way. I put the key in the ignition & stared the engine but none of the windows will now close. I have had to tape bin liners over the windows as it started to pour down. Could anyone please offer any advise as I have got my car booked in for its annual MOT on Thursday Many thanks