My girlfriends 2002 A6 quattro got totaled due to a similar water related issue. She hadnt driven the car for just a week, and after some heavy rainfall that week, the car started and stalled immediately. All of the windows were closed but water still some how leaked in. The rear right passenger floor had 4 inches of rain water sitting on it. We towed the car to the dealership and they couldnt do anything to help. Car was damaged beyond repair by the rain.
Needless to say i took my own 2002 a6 in to have the drainage cleared soon after. Once bitten twice shy...