I figured out what the problem was.
I changed the virtual directory on the new install to "HelpDesk and SelfService" from "AdaxesHelpdesk and AdaxesSelfService". Deploying back to the renamed virtual directory was failing.
I can change the Virtual Directory and Alias after the restore but I'm left wondering if that's such a good idea...
Is there a supported way to change the alias/Virtual Directory on a new install and apply the backup of the ui config to it?