Their is nothing to save it's not like there is any inventory. Just start 4 with a start at new content and have all old content be unlocked as it would have been. That is simple enough to do.
Yes, it will be solved. If you choose "Submit" (instead of "Rebel") at the end of Chapter 3, make sure you continue the game after the credits and "Go to Sleep" (without Ona or Neko) during the night. At that point your choices are automatically saved.