So my company uses OneNote for many things. We have a user that has it one his desktop computer and his iPad. I'm not sure how long it hasn't been working correctly for him but he says that it's not syncing at all for him anymore. I took a look at it to see if I could figure it out. His desktop seems fine, however, his iPad reveals a message on the top in a yellow bar underneath the toolbars: "Merge Conflict - We couldn't merge some changes. To review conflicts, use OneNote on your computer or OneNote online."
I had him sign out of OneNote on his desktop and on his iPad and log back in (both, to ensure he is using the same account for both, and to see if that fixes the issue). It didn't work.
He is using Office 2016. If you need more information, let me know.