This is exactly our scenario as well. Attempted an upgrade from 4.1 to 5.1 and like most of our other vCenter upgrades it failed to upgrade the database. It was just easier to start over and add all of our clusters, hosts, etc. back in. I tried the above powershell command in the VMware PowerCli with just one VM and it worked perfectly so fingers crossed that it'll work using the "all VMs in vCenter" option. Thanks!
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