by Emma Richardson.
I had this happen once before but it was when I was backing up to an external folder. Moodle couldn't write to the folder so it randomly put them somewhere else (I think in a backup folder in moodledata maybe) and still reported that backups were ok, which I found really curious. I guess I would check your permissions on your moodledata folder, see if they run tonight by chance and also look for backups (search for .mbz files) having been randomly saved somewhere else.