...some notes are still there, but not all. I have cloud backup of my entire user folder; where can I find the old notes?
Open System Preferences > iCloud
Deselect the box next to Notes then reselect it.
Give iCloud a few minutes to re sync the data.
it says all notes will be deleted from Mac - proceed? I also should have specified that my backup is not in iCloud, it's a non-Apple cloud service. up there is a file called 'NotesV1.storedata' which I figure must be my old notes?
Retrieving data ...