Why is this an issue? This is basic Moodle management, which is an extension, or refinement, of basic HDD management.
What I have implemented is an annual cull of my Moodles. What courses are active, what are not? What courses have been edited and so on. The regular backups take care of most of those issues, but twice a year I take a archival backup of all courses, place them onto Blu-ray discs (used to be DVD, and CD before that) for longer term storage. NO courses are deleted outside this specific period. ALL courses are burnt to disc and the inactive courses are deleted AFTER an off-server backup is made. All backups are then deleted as well. That is the only time courses and backups are deleted. Permissions are set to remove the delete courses capability from anyone other than the admins so courses cannot be accidentally deleted. Any other course delete required, and it has happened where someone built a course without getting any of it right, can only be done by an admin and everyone who needs to know is told. Ok a layer of bureaucracy, but it works even if it slows the process a bit.
These policies are applied automatically to Reset as well.
While this means I have to spend part of a weekend burning to disc, then storing the right discs in the right places for others to be able to access, it doesn't take too much time for me.