Auto Warranty?

Car is 39,000 miles, warranty expired at 36,000 miles.

While traveling in the rain, the front passenger floor became saturated with water. I took the car in to the dealer. They sent the car to a body shop, which found the leak and sealed it. $275. Not a big deal so far.

The body shop guy said there was water sitting in the hinge pillars and rocker, and he was certain the leak was present for a long time before any water came into the cabin. In fact he said it was probably there in 2012 when we purchased the vehicle. When those areas finally filled completely with water, they overflowed into the cabin. But we didn't see any signs of it, so we didn't take it in for service on that problem.

If it can be credibly demonstrated that a problem existed before the warranty expired, what are the chances/difficulty of getting the manufacturer to honor the warranty? The problem is it's $1,000 to replace the carpet, and now I'm real concerned about the damage done from the water sitting inside the frame.