Clutch gone already??

Ok, so my car is in the shop getting some major repairs (hit a nasty pothole that cracked the oil pan = blown engine etc…) everything is being covered by insurance. Yesterday, my service advisor calls to notify me that the clutch on my 2003 GTI with 21,000km’s is 90% worn out. He recommends that it be replaced now since they have the engine and tranny out of the car, they would charge $900! Let me be the first to say that I baby this car and never abuse the tranny. I told him to forget it and put the old clutch back in. My question is, could the clutch seriously be worn at 21k’s or is this bs so they can make a little extra coin seeing as they have car the car all apart? Is their any chance of getting this fixed under warrenty?