A family of Microsoft products that enable users to capture, organize, and reuse notes electronically.
I finally fixed it!, thanks to this reddit thread:
I had the exact same issue with OneNote ghost notebooks under:
OneDrive » ^.Documents
The notebooks were already deleted from OneDrive, they were not visible in OneNote web, and clearing registry/cache/MRU folders did not permanently fix it. They disappeared when I opened OneNote offline, but came back immediately after reconnecting to the internet, so it was clearly being re-synced from account-side metadata.
What finally fixed it for me was using OneNote 2013 in a temporary Windows 10 VM.
Simple steps:
-> Create a temporary Windows 10 VM.
-> Use a local Windows account in the VM. Do not sign into Windows with your Microsoft account.
-> Install OneNote 2013 inside the VM.
-> Open OneNote 2013.
-> Sign into OneNote only with the affected Microsoft account.
-> Go to File > Open.
-> Find the ghost notebook under OneDrive » ^.Documents.
-> Right-click the ghost notebook and choose Remove from list.
-> Repeat for every ghost notebook.
-> Close OneNote 2013.
-> Open normal OneNote on the main PC and check again.
After doing this, the ghost notebooks disappeared from my current OneNote as well and did not come back.
My guess is that OneNote 2013 can still remove an old legacy “recent notebook” cloud pointer that newer OneNote clients keep re-syncing but cannot properly delete.
Use a disposable VM only, because Office/OneNote 2013 is old and unsupported. I would not install it on the main machine.