Over the last couple of days we have also started to experience the same issue. I deployed 5.6 a year or so ago, then upgraded through 5.7 and later 5.8.1 without any issues. We haven't changed any configuration settings since then for either the collector user or the vCOPs license, however recently (..and it may be unconnected) we decommissioned several datastores and added some new ones. Since around that time we started seeing a problem where some datacentres cannot be drilled down into, whereas others can. Our vCenter permissions are applied right at the top of the hierarchy (on the VC object itself) and the propagate option applies exactly the same set of permissions to each of the datacentre objects. Some standalone hosts in the root of the hierarchy can be seen, whereas others cannot.

We have approximately 80% of the inventory items missing now. I unregistered and reregistered the vCOPs solution with vCenter which was successful, but didn't fix the problem. Further to this I restored a backup of the original appliance that was around a month old, and this also has the same issue. There would appear to be some vCenter inventory related issue going on which might have occurred when we added new resources recently, however all of the vCenter health checks work out fine so I'm at a loss as to what has caused it.

Finally, in order to prove whether the issue is VC related I've just deployed an entirely fresh set of vCOPS UI and Analytics VMs - then registered/licensed correctly and confirm exactly the same behaviour is being experienced.

Does anyone have any ideas about where to look next?