Ok, now there is a good reason for complicating one's Moodle 'life' ... testing/learning new add-ons/plugins - info not disclosed before and cannot be aquired via 'Vulcan mind meld'! ;)
Somewhere in these you mention failure of automated backups? and Moodle not being able to finish nor clean up. Known issue if the course backups get 4Gig +. Relates to operating system limitations which on remotely hosted shared system might have other factors as well. After Moodle creates the backup zip/tar.gz by mbz name, the code uses 'copy' to move the backup file to destination ... could be filedir, could be filedir + other, or just other. In any event, the OS has an issue with 'copy' ... if one had command line access one could find the completed .mbz file and 'MOVE' it to a location with no problem but even as super user a 'cp' command fails. Not sure there is a solution to that although the default of using tar.gz in backup as opposed to zip for the .mbz file has solved it somewhat.
As far as Moodle not cleaning up ... any process that ends before completion would/could not know if it needs to clean up or not. Nature of the beast, am afraid. Sometimes manual clean up is needed/required. Those things that involved files in the new file system as you know require both manually removing records in the DB but also in filedir (VERY CAREFULLY).
The desire for 'all system administration procedures working smoothly and reliably' always a goal ... forever changing as one marches Moodle upwards.
BTW, may have a 'badge', but that doesn't say how many times the owner of that badge tried something and failed ... this to say, have more experience with what NOT to do than most! ;) A long the way, however, one learns some 'backdoors'/other ways of arriving at destination.
'spirit of sharing', Ken