Hmm, I would probably not allow saving while the wait is happening. Either set a variable when the wait starts so "save" knows to wait, or set a variable when "save" is clicked, and start saves after the wait, if that variable is set.
Other than that, I would imagine you would need to store that the wait is underway so that when reloaded, you could detect it, and manually perform what should have happened.
Sorry I don't have a solution, but hopefully I sparked some ideas.