From what you have described, IF you did not download course backups, moodle code has done what it's been told to do with the preferences set in course backup defaults and auto backups.
Think the keep # is affected by other settings ... like 'change since last backup'.
No am not saying there is a bug in the process.
If you didn't catch this issue before auto's were made ... and old backups removed from view, the only hope is to see what's in moodledata/trashdir/ that has mimetype of Unix compressed gzip file - files in moodledata/filedir/ and trashdir are not in humanly recognizable file names - but a hash.
There is no admin link that does that ... nor plugin (me thinks) ... has to be done via command line (no offense, but you don't sound like a CLI person).
'SoS', Ken