My organisation (5000 users) had made a decision to move from OneNote 2016 to OneNote UWP. We are trying to work out the best way to move notebooks from local storage to OneDrive. It doesn't appear that doing so automatically is achievable. The next best method looks like using OneNote UWP to find local notebooks to move to OneDrive.
I have logged a call with Microsoft and they have said that OneNote UWP is "hardcoded" to find local notebooks in the default location only, I.E. c:\users\username\documents\onenote notebooks. I have tried this but still no luck and MS seem to be out of ideas.