Retiring and Deleting Applications
When you know that you will no longer need to create new deployments for an application, right-click the application and select Retire. When you retire an app, you can no longer create deployments for that app, unless you Reinstate it first. Retiring an application does not affect existing deployments, only new deployments.
To delete an application, you must remove all references to it. References such as dependent applications, active deployments, and dependent task sequences can affect the ability to delete an application.
Remember that you can export an application (with or without associated content) and store the application on a file share, in case you need to restore it at a later point.