If deleted OneNote notebook still shows in your OneNote for Windows 10 (UWP) application......

Yes. I'm sure so many people experienced it. You surely deleted your notebook from OneNote for Windows and OneDrive, but if you click More Notebooks you'll see your deleted notebook is still on the list. What's more, if you try to open them, it says OneNote failed to open them. What the hell?
So called Phantom Notebook by someone, this is quite a nuisance. And I'm sure you may also have seen a lot of "solutions" when you have MS Office 2016 - clear Recent in OneNote 2016. Well, the problem arises when you don't have MS Office. And everyone will agree that it's quite too much to subscribe to Office 365 to remove the list......

But did you know that there's one more location where you can access and clear that Recent? You can't find it in OneDrive. It's on Office.com.

Oh yeah. https://www.office.com/ ← Log in here.

If you visit the page and log in, you'll see the list of recently opened documents, and you can also see your deleted OneNote notebooks. You can safely remove those 'phantoms' by clicking ... icon in the middle of the list; after that, go to OneNote Online or OneNote for Windows 10, you can see your list is finally clean now. :)

Hope this helps if you're uncomfortable with it.