OneNote Stopped syncing. We can't sync this section because the server isn't compatible with this version of OneNote.

I have followed up with the OneNote team to see if there is any update. This may be related to the issues we are seeing with other Office apps on Mac and opening/editing files that are stored to OneDrive. 

-Jesse

Jesse, for what it is worth.  I am also randomly experiencing strange behavior in Word and Excel when editing files on OneDrive.  Intermittently OneDrive files will refuse to open for editing and only open in Read-Only mode.  This has been very random and intermittent for me, so I haven't reported.  But, since you mentioned it, I thought I would share.

While attempting to further diagnose this issue, I had a small breakthrough.

While attempting different things to night, my existing notebooks on OneDrive began synching after I re-enabled Files On-Demand (further context for it being off is provided below).  Although my two OneDrive notebooks are now synching again, my existing shared notebook that is an Office 365 Group SharePoint location still will not synch.

I haven't had time to prove whether this was coincidental or a true root cause, so I'll be very interested to hear whether this makes any difference for the other users experiencing this issue.

Additional OneDrive context... around the end of February or early March I ultimately had to turn off OneDrive Files On-Demand.  My OneDrive client, which also happens to be an insider version, was constantly hogging my CPU and, more importantly, destroying my battery life.  I tried several potential resolutions from the forums, including a complete reset and re-install of OneDrive, but there was either no change or the behavior returned after 12-24 hours.  Turning off Files On-Demand solved this issues.  Prior to tonight, that feature has been off since.

I have followed up with the OneNote team to see if there is any update. This may be related to the issues we are seeing with other Office apps on Mac and opening/editing files that are stored to OneDrive. 

-Jesse

I wish I could help you who are still having trouble but to be honest I'm not sure how mine started working but it has been for the past few days. I haven't had an update come through for me for at least week. Here is a screenshot of what build I'm on.

Exactly the same situation for me - Multiple Notebooks, all displaying the same sync error. (6.24 (19032003)

Insider Fast Build Tree

We can't sync this section because the server isn't compatible with this version of OneNote. (Error code: 0xE000078D bfuqa)

I'm currently on 16.24 (19032003).  I checked for updates this morning and nothing is available.