I'm currently on the "Secrets in the Air" mission, and the game hasn't saved my progress since then.
I finished the mission, went to sleep, and then tried to quit the game, but nothing happened (I got the grappling hook and used it a bit).
Then I restarted the game and progressed quite a bit further, completing 2 or 3 more missions (about 2 hours of gameplay). Now I'm back at this point again.