I'm having the same problem. After I play for a few hours the "save state" stops working correctly.
As long as I stay in game, I can continue to save and load. After a few hours of playing, something goes wrong. Once I exit the game, then try to go back to my library, it says it's empty. I have to refresh the page. Then the library returns. But all of my resent saves are gone. Only my earlu save from shortly after starting the game works. It seems like it loses connection with OneDrive at some point. Maybe it times out? Hope this information helps.
I love what you have done. Once the save state issue is fixed, nesbox will be amazing.