Not sure it'll help but..
When I typically update, I save the published game to the "desktop" and then log-in, "edit this listing" first, update, and then go back and upload it over the old one. It should auto-update. Since your game is particularly huge, it might take your browser some time to upload it, especially if Quest is receiving a lot of traffic. Try restarting your browser, empty all the cookies, and then log back in during off-peak hours and see what happens

But the new upload SHOULD replace the old file. The plays will remain the same though.