I'm Galit from the QE team of VIN.
All the things that you've described are correct.
It is actually an edge case where the only VM, that the manual App can be managed from its Map view, was removed from the App.
The Manual App management is as designed, and may be changed in the future.
There are 2 ways to overcome this situation:
1.You can, as you stated, create another Manual App with similar name and remain with the "Zombie App".
2. To run a specific command that will remove the Zombie App from the DB.
Please note that option no. 2 involves using an API that we do not publish.
If you would like to use option no. 2 contact me in private and we will see about supplying the relevant commands to run in order to delete the "zombie" application.