I guess you want to keep the app in source system and want to delete in the destination system.
In that case, copy the existing app into a new app. Based on the package assignment for the new app, this might require a new transport.
Now that you have the backup of the app, delete the app. This will ask for a transport for the delete action. Create a new transport for this. Release this new transport. This will delete the app in destination system as well.