I have old backups for VMs that I have since deleted. Can I just safely delete the folders under /mnt/datastore_name/VMID ? A lot of backups so command line is what I am trying to do.
That is the Garbage Collection, it basically removes chunks after a day that are not referenced by any index files. And what you are deleting are index files, so if chunks were only referenced by index files you deleted, they will be removed by GC after ~1 day.