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Hi FedeleC, I had the same issue with the latest version. Well is not during the upgrade process , but we saw in the controller.log many line...
I had that error earlier and I had the key. Once deleted in my template and re-apply to my target VM it work.
You should read about the feature "Use RemoteApp if available" option and enable or disable depending of your setup and try again your publish...
When I disable logon on a specific server and reboot this server later it automatically enable. There is a way to keep the server disable after...