Is there a way to permanently remove unused apps from the MDM? If I right-click an app and choose Remove Mobile Application Package it will only be gone until the next time VPP Licensing Data is synced again, and then it will reappear on the list. There are quite a few that were added early on that are not used anymore.
There is a check box where you can add VPP tokens that will automatically create packages for you. With this checked it will reload all apps that you acquired licenses for. If you uncheck this, you can remove them, but you will have to manually add any new apps as they are acquired.
So where is this place you speak of to add VPP tokens for auto-create packages?
In Server Settings, MDM Tab, Apple VPP Licensing Accounts, highlight an account, uncheck the "Automatically create packages for licensed Apps"