AAAAGH! Took the trailer in for some warranty work and they discovered some small holes in the roof along the side. Best guess is that we scraped against a low hanging tree or branch.
So, if I had realized this immediately or at least the same day, I probably could have at least temporarily fixed it myself with Eternabond tape etc. BUT since it has been raining so much, I didn't get up on the roof. Now the dealer believes that the entire roof membrane should be replaced. Looks like our insurance will cover it. My concern is whether any water got into the roof because of this since I have no clear idea as to when it could have happened! That's why I'm in favor of replacing the membrane so we can be sure any other resulting issues can be addressed.
Lessons learned - look up more often and ALWAYS check the roof after traveling, especially when you have been driving through a state park or other area with tall trees!