Sounds like a job for progressive with delete rsync only on the filedir directory of moodledata to a large archive drive.
First dry run to see how long and how large. Then run for real. First run will take a long time and acquire it all, but progressive with delete from that point on would update the 'backup' with only files that are new and the 'delete' would compare what's in filedir with what is archived and if a flie has been deleted in filedir, the same file would be deleted in the rsync'd drive.
See man rsync.
'spirit of sharing', Ken