Not sure if there's anything this mod can do about it, but Chinook sometimes gets stuck in a specific place on the map and eventually despawns.

If I drag it away from that spot via Telekinesis, it flies right back there.

It's almost like its pathing is dead-ending at that spot or something.

I've seen this before. Basically when the chinook is done, it will select a point 8km away, go there, then wait to despawn. Sometimes that point happens to be on land. Old Rust bug.

I probably won't do anything about it now. The plugin just overrides the path finder, whereas fixing this would require overriding the brain states.