If I understand correctly, the standard procedure for storing backup files would be for moodle to place the backup file in the temp/backup directory for a while, and then give them a hash type name and stick them somewhere in the filedir folder. This seems like a strange way to handle things, but that would explain why all my backups seem to be randomly sprayed around in the moodledata folder in different subfolders.
If I have this correct, then the backups made today will remain in the temp folder for a short while, then they too will be moved to some random folder in the filedir????
I fully understand your advice to avoid messing around in the file system like this. I am trying to find the best way to solve this problem, and, by replacing the large backups with these small, "dummy" files, I have been able to clear enough space on my server to actually get a recent backup of each of my courses, which is nice.