Just found out there is a known issue with removing datastores in and out of datastore clusters. In vCloud Director 5.1 this was working fine. vCloud Director refers to storage via storage policies (formerly profiles) so you could on-the fly change the datastore cluster structure (as long as all datastore inside had the same storage policy).
However in vCloud Director 5.5.1 if you move a datastore in or out of a datastore cluster, vCloud Director will loose it. The fix is described in KB 2075366 and involves clean up of vCloud Director database inventory data.