To get around it quickly, I did the following (basically rebuilt the whole thing):
- Export all the notes (in jex file format)
- Created a new profile on the desktop
- Imported all the notes to it (which created "/App/Graph 2" on OneDrive)
- Confirmed it was all there
- Sync'ed it with Mobile phone
- Erased "/App/Graph" from OneDrive
Although, the sync does seem a little flaky. It'd be nice to figure this out, so we can prevent it in the future and/or resolve it in a better way.