I recently had a problem with one of my two vCenter servers in linked mode. When using the vSphere client to connect to this particular server, the client would not show the hosts/VMs or anything about the 2nd vCenter server.
But when connecting with the client to the 2nd vCenter server, it would show both vCenter servers and their hosts/VMs.
So obviously something is up with the first vCenter server. I ran the Linked Mode setup again and it acted like it wasn’t linked, which was how it appeared. So I went through the prompts to set up the linked mode and when it came down to actually setting it up, it would fail. It did this twice. Looking at the log that it mentioned, it was complaining that the vCenter Server service was not stopped. It had successfully stopped the Web Access service, but not vCenter Server.
I loaded up services.msc and went to stop the vCenter server service but was prompted that our Site Recovery Manager service would also need to be stopped. After agreeing and stopping both services, the Linked Mode configuration completed successfully and started the vCenter Server and Web Access services. It did not however start the Site Recovery Server service.
At this point it looks like the Linked Mode configurator needs to understand about other services that depend on vCenter Server and track them to stop/start before/after the linked mode is configured.
I don’t know why the vCenter server became unlinked from the 2nd one, but it works good now!