I had a similar problem getting the following error message when I tried to "Send to OneNote" to save an email or meeting from Outlook to OneNote:
"Error when expanding notebook. One or more of the document libraries on the user or group's OneDrive contains more than 5,000 OneNote items (notebooks, sections, section groups) and cannot be queried using the API. Please make sure that none of the user or group's document libraries contains more than 5,000 OneNote items. Browse to this page for more information: https://blogs.msdn.microsoft.com/onenotedev/2016/09/11/onenote-api-calls-fail-with-a-large-number-of-items-in-a-sharepoint-document-library/".
Since my company security policy did allow me run the Microsoft program to determine how many notes I had on OneNote repositories on SharePoint, I had to find another way to fix this error.
After multiple Microsoft help tickets and multiple conference calls, I fixed my problem by moving all my documents / files from SharePoint-"My Documents" and SharePoint-"My Downloads" onto my local disk drive. Once the number of my files located on SharePoint was well below 2,000, I was able to "Send to OneNote" (emails and meetings) from Outlook to OneNote.