I have about twenty OneNote notebooks that I use in desktop OneNote and 3 had stopped syncing (probably due to me manually killing the sync service – but that is a different story).

To fix this

1. Close the problem notebook
2. The system will warn you that parts of the book that will not sync will be moved to a new notebook called Misplaced Sections which will appear at the bottom of your list of notebooks – accept this solution if prompted.
3. Close OneNote
4. Reboot
5. Wait a minute for OneDrive Sync to get up and running again
6. Open OneNote
7. Login to OneDrive on the web and browse to your OneNote book and open it in Desktop OneNote
8. Allow syncing to complete
9. You now have a working syncing copy of the OneNote book
10. Open “Missing Sections” and Move, Copy or Merge the content back into the original document (Merge is to be preferred).
11. Having Merged, OneNote may indicate page conflicts. Manually fix these by editing, copying and pasting and then delete the conflicting pages.
12. Allow syncing to complete and then close OneNote.
13. The goal is complete.