I’m having the exact same problem, except checking the “can be main nav data” in recast does nothing. I could work around this except the problem also still persists when I package the game as well. Was there something else that made yours work maybe? I also noticed that changing anything in project settings overwrites the same thing in all my recasts per each world.
I’d appreciate any help as this is game-breaking 
edit:
Ah, I see, you cant touch “can be main nav data” checkbox in project settings AT ALL after starting. Doing so will for some reason prevent it from working, even if you have it checked on your recast as well. This is a really dumb annoying bug.