+ 1 to what Howard has already said/suggested.
moodledata/filedir contains all the files uploaded to moodle ... teacher uploads as well as student uploads. It is very important to back it up. Files contained therein are not 'humanly recognizable' and it's wise to backup the database for Moodle as it contains the meta data that eventually become humanly recognizable links/files.
If you are asking those sorts of questiona about cron, might be that it's not setup. Important that it be setup cause one of the task/jobs of cron is to automagically 'empty' the trashdir which contains files no longer linked anywhere in the moodle site.
Please see: https://docs.moodle.org/33/en/Cron
Been my experience (depending upon factors), that rsync'ing moodledata/filedir/ contents is minimal backup and all that is needed, as Howard has already said. rynsc would bascially mirror what's in moodledata/filedir/. Initial run of rsync would take some time, but if one sets up incremental rsync after that, only new files added to moodledata/filedir/ get copied to the location of the rsync'd directory backup and any files that have been removed from filedir are also removed from the rsync'd directory backup. The incremental rsyncs go much faster.
For details on rsync, if on Linux 'man rsync' should provide what you need or do Google search for your platform and rsync.
'spirit of sharing', Ken