I recently had several customers contact me and ask about an error they were seeing when trying to create a new OneNote Notebook.
When they do this onenote.com will open, but it will throw an error:
"OneNote can't display some of your notebooks. Please try viewing them on OneDrive for Business."
This is caused when OneDrive contains 4,999 or more files.
5000 items is design, the below KB touches on it
"The number of items in this list exceeds the list view threshold, which is 5000 items" error when you view a SharePoint Online list in Office 365 Enterprise
If you drop this to 4,998 files, you will not see the error.
Keep between 0 and 4,998 items on OneDrive.