I wonder if your notes were borked out of session.xml, but the files were still available at AppData\Roaming\Notepad++\backup.
I've changed machines where the user profile was in a different location, copied my AppData, and replacing the old location in Notepad++'s session.xml was enough to restore my unsaved notes.
Of course I tried everything (except looking in the shadow copy? Don't remember), but in the essence the shutdown triggered Save All workflow (somehow) and I responded with 'No'.
I've changed machines where the user profile was in a different location, copied my AppData, and replacing the old location in Notepad++'s session.xml was enough to restore my unsaved notes.