When deleting or moving the last module of an application you are presented with a dialog box with the following text and options:

"You are about to remove the last module from '<application>'. This will delete the application.

Do you want to proceed?"

1) Delete

2) Don't remove module

There should exist an option to "continue by removing the module but don't delete the application" with a shorter text of course, like "DON'T DELETE".

This also would be consisted with the fact that I tested and it's possible to create in Service Studio (version P10) a new application without any modules.