Previously published RemoteApps can be removed from the RDWeb via regedit
HKLM\ SOFTWARE\ Microsoft\ Windows NT\ CurrentVersion\ Terminal Server\ CentralPublishedResources\ PublishedFarms\ <RDSCollectionAlias>\ Applications
Simply delete the registry branch relating to the orphaned RemoteApp.
You can also enable or hide the full server desktop link from RDWeb via the 'ShowInPortal' key found in...
HKLM\ SOFTWARE\ Microsoft\ Windows NT\ CurrentVersion\ Terminal Server\ CentralPublishedResources\ PublishedFarms\ <RDSCollectionAlias>\ RemoteDesktops\ <RDSCollectionAlias>
