Try the following. Some situations this works for me and may work for you:
Create an app, with the same name and type as the one you deleted.
(If you are using Scriptcase internal versioning function, make sure you do it on the correct and same version that the defunc application was on, as the link in scriptcase is project+version+application)
Then delete the app again.
The idea behind this is that scriptcase will create the links for the app to the internal tables that handles settings, applications and event codes in the scriptcase database. I have a suspicion that those links broke when you deleted the app and all tables were not updated correctly.
If you get an error when you try to create the app again, then one will have to go another route. But suggest trying this first.
Also, side note (One I learned the hard way): ensure you have enough disk space at all times. Especially on Windows. If you run out of disk space, your netmake_db will be corrupted, and it’s a pain to get it going again. (Especially if you don’t have proper backups).