I just added dropbox on my iPad (a blank new Dropbox account), my iPad had a mobile notes file and did a sync. Then I added dropbox onto my desktop app, and I had a desktop notes file with a different name and did a sync. After syncing my notes and highlights from the desktop app (which was most of my notes).
I am not sure what has happened. I have bouts of feeling, I should use the "User notes" feature more, it seems helpful. And bouts where I want to keep my files separate. I believe this instance has settled the matter for me. It seems best that users avoid any feature in Accordance that could be impacted by synchronisation. Especially if you feel like your user notes have any value what so ever.
(And before anyone tells me that I can undelete drop box files, I have already checked, dropbox indicates that there are literally 0 deleted files in this new blank dropbox account.)