Dear respected Brad Semenko,
Good day! Thank you for posting to Microsoft Community. We are happy to help you.
I’m sorry you’re having a problem with OneNote Sync but based on your description we can work together to resolve it.
For the situation you encountered, we deeply understand the inconvenience caused and apologize for it.
First, may I know are you using OneNote 365 app (formally called OneNote 20216) or OneNote Windows 10 app?
As you mentioned, "I have tried to copy sections into a new notebook only to have the problem reoccur" may I know did you copy sections into a new notebook in a OneNote desktop client app? If yes, and since you mentioned, "I can open the notebook via the web app but the sections that do not synchronize show an error." then you may try go to OneNote Online create a new notebook in OneNote for web (online app) first, then copy and paste all un-synced notebooks in OneNote Online, make sure they all appear in OneNote Online.
(I understand it will spend some time manually copying all un-synced notes to OneNote online, but this will reduce the risk of losing notes. Appreciate your understanding.) then click "Open in desktop OneNote" from ribbon to open it in OneNote desktop client app. See if the error message will disappear.
If above doesn't help, for further troubleshooting, could you please share information below?
1.Where do you save notebook? Personal OneDrive or OneDrive for business?
2.Screenshot of error message encountered.
3.The version of your OneNote application.
3.Are you using OneNote 365 or OneNote Windows 10 app.
Appreciate your patience and understanding and thank you for your time and cooperation.
Sincerely,
Waqas Muhammad