I had a problem where my heaters just stopped blowing air after a few day it done my head in no hot air no cold air I could here the fan and motor working all motors and flaps working I then remembered I topped my water up with anti freez i looked at my water level noticed it was a bit high just above the sensor after draining a little water so it was below the sensor and checking my heaters again thankfully that done the job all working now I've seen people having the same issue I advice you do what I done I was quoted 200 pound from Audi to check my car 

That's very odd Nathan. Having a high level in the water reservoir does not normally affect the fan. I wonder if you have a faulty level switch which is somehow interfering with the electronic control system.