Had a windstorm and my shingles blew off roof, what to expect from adjuster?

I've had my homeowners policy for almost 4 years and i haven't had any claims until last week when we had a huge windstorm leaving a lot of shingles blown down. A friend of mine noticed that a lot of the wood on my roof is rotten. He thinks it is coming from a tree that is tall and the branches branch out on the roof. I'm just wondering if the insurance company could deny my claim bc of the rotten wood because i don't know how long it has been that way maybe they could call it pre-existing idk? I know my policy covers fungi and dry rot though.