Hi, I left my windows open during a big storm I did get to it fairly quickly but a lot of water got in, the drivers side footwell is very wet and the passengers side is slightly damp. 
When driving it yesterday some lights were flickering and the parking brake malfunction warning came on after a few minutes the car cut out and wouldn’t restart. I have changed the fuses which were damaged and the car starts however, the warnings come on after driving it. I’m currently drying it out just wondered if anyone has any advice or ideas on the sort of damage this could have done and where to go from here, any help would be appreciated, thanks! 

I would say get it dried out & find somebody who can run a diagnostic scan..   probably followed by a chat with an auto electrian...  Its not something that has happened to me, but its what I would do. Hopefully it will dry out along with any electrical gremlins.. Good Luck

Thank you, it’s drying out quickly in this weather! AA did plug it in and showed up an issue with the central control module. 
Just a waiting game at the moment I suppose! 

The only downside with the A6 is the costs when something goes wrong...  

Water mdy have got in via the pollen filter housing or battery tray if drain holes are blocked. Also consider leaking window or sunroof seals.