I was just fooling around with an On Prem installation of D365 and I created a custom app to test out converting the legacy Web Interface application into a Unified Interface application. When I was done testing, I wanted to remove it, but I saw no where in the App Designer to do that.
THe solution, it turns out, is to go into CRM under Settings > Customization > Customize the System. Under the list of Components, you'll see "Apps". Simply go in there and remove any apps you don't wish to have anymore
I did a Publish All Customizations just in case, but likely you don't have to do that.