When you delete an application object from the design-time application and deploy a patch, the Data Integration Service does not delete the object from the run-time application. In some cases, the deleted object might be an affected object.
If the wizard identifies a deleted object as an affected object, the wizard will attempt to propagate changes in the deleted object's child objects to the deleted object. The wizard will also attempt to validate the deleted object. If the deleted object is not valid, you cannot deploy the patch.
If users are not running deleted objects, redeploy the application to remove the objects from the run-time application.