Heard of this before from other Winnebago owners when we owned a Journey. Winnebago is likely to tell you that unless you can prove that the seam where the edge of the roof fits into the aluminum channel was inspected/recaulked every 6 months since coach was new, there is no warranty. It is a poor design. There is only about 1/2" of roof material in that little grove and if the caulk give up, it can come out. Many of us used Eternabond tape on that seam to keep this from happening.
I would be taking it back to the dealer for repair if that was the case or calling my insurance company.