by Ken Task.
How often is your cron job (and thus task that clean up areas of files in moodle) running?
Leave DB alone ... note some references are to recyclebin for deletion of a course category + courses contained therein if you choose that option. The . records kinda like from OS and ls ./.
The file -b for the contenthash ... in your table shared didn't see if that contenthash matched up with anything a . row or one of the .mbz files in moodledata/filedir/
Even if moodle were creating 0 byte files, no space is taken up and counts only vs inod limits of server.
Suggest running cron ... several times from cli until it shows it did nothing ... all caught up ... and then use the file -b command again to see if 0 byte file gone.
'SoS', Ken