Advise installing moosh ... http://moosh-online.com/
A couple of it's commands:
http://moosh-online.com/commands/
deal with missing files, orphaned files, etc..
file-datacheck, file-dbcheck, file-list
Do you hide courses? Are students (and their submitted assignments) still in those hidden courses? Did the teacher of that course make any backups of that course (or do Teachers make any backups at all?). Those backups are in Teachers 'private files' and you, as an admin level user, even if you visit the course, won't see those Teacher private files' backups.
Funny you should post this today of all days .... just spent 8 hours today on a site that's pretty much been neglected for about 2 years now. 2TB data drive had reached 90%+ with some courses over 130Gig.
What a mess! :\ About 500 courses have to be inspected.
Moosh has been a handy/helpful tool.
'spirit of sharing', Ken