If you Delete an active internal application, it moves it into Status Inactive rather than permanently removing the application. Upon attempting to upload a new version of the same application, the AirWatch console sees the application has the same app ID and the “Add Version” behavior will display.
To fully delete an application from the AirWatch console, navigate to the section for Inactive applications, and delete the application a second time.
This issue has been given identifier PR-187540. We are working on clarifying this process with an update to the AirWatch console.