This assumes you have read our getting started article on updating an WebSphere application.
Replacing the entire application is just like deploying the EAR. Typically, it makes more sense to follow the normal produce for a deploy using the WebSphere admin console or using the monitoredDeployableApps auto deploy. Or, you may have a deploy technology being used, such as Anthill or Jenkins.
In this example, the app is being replaced with the app packaged in devWASDelta001.ear.