do you have any folder stuctures setup in your VM's and Templates View? If so, when you disconnect and remove the hosts from vCenter, then add back, all the VM's go into the default "Discovered Virtual Machines" Folder.
The proper procedure would be to evacuate all your VM's, put the host in maintenace mode, then remove host. Once the host has been removed, add host back using FQDN... rinse and repeat.