I had an issue where I was removing datastores and was getting errors about the datastore still being in use or that it was waiting for VMs to be migrated off. It took me a while to realize there were references to vCLS VMs on the datastore. I had to log in as the vsphere administrator to see these and I could not delete them through normal means.
See https://kb.vmware.com/s/article/80472 “Retreat Mode Steps” to disable DRS in vcenter for the cluster with the orphaned VMs, which will remove the references, and then re-enable DRS. Pay attention to the cluster number, it should be in the form of domain-c1006
Andy's Brain 