Thank you. We're getting closer, but we're not there yet.
On https://onedrive.live.com/ it appears that I can see my OneDrive file system, including the directory MyFiles > home > Documents. The shortcuts to notebooks that I can see in File Explorer do not appear. There is no sign of the OneNote files. However ...
If I use the "search everything" in onedrive.live and enter the name of a notebook, called Journal in this case, a drop-down appears containing a folder icon along with the word "Journal", but no location given or "go to location of folder". So it seems that the notebook is there somewhere. If I click on the icon a web view of Journal opens up, and indeed, it is the correct notebook. The URL at this point is onedrive.live.com, not anything like "office365" or "onenote.com". At the top of the page is the name of the notebook with a drop-down arrow. Clicking that gives a location, as shown here:

But if I click on "Documents" there, it takes me to MyFiles > home > Documents in which, as I mention above, the notebook is not visible. It seems to me that the notebook files must be there, but onedrive.live is choosing not to show them. We already know that onedrive.live is not showing the shortcuts that live in that directory.
Does it sound to you that that's the issue? That the notebook is there, but onedrive.com is not showing it? If so, how can I get it to show up?
Relating to my vent above: I Googled "show onenote file in onedrive.live", but the returned hits are for OneNote 2016!