There is one other possible ... IF teachers were not removed from the system, they could have, by themselves, backed up their courses and saved to private files (if any didn't trust the system and they had the ability to do so). DB query would be the only way to see that. OR, logging on as one of those teachers to see what's in their private files.
As far as plans for autobackups ... more adventures await.
For me ... I'd advise setting autobackups to save backups *outside* of filedir ... to a designated directory. There are issues with that, but at least one will not have to navigate the maze of the new file system - one can see the backups by a humanly recognizable name which has course ID and short name of course in it. Also remember, that the settings for backups (defaults ... what to save in the backup) apply to autobackups. So if NO USER is set, then the autobackups will have 'nu' in the file names.
If on Linux, check out the command line scripts that are in code/admin/cli/ There is one for autobackups and one for backing up courses individually. Both can designate another directory outside filedir.
On some sites I help manage, a few courses have gotten so large the only way to back them up is via command line and those scripts. I have a 'special' bash script in moodlecode/admin/cli/ that uses the php scripts at that location and backs up just those courses.
'spirit of sharing', Ken