You need to deploy the entire application again.
You cannot selectively update parts of it.
However, you can use multiple versions at the same time, for example, to test the most recent changes before passing them on to the public. Each version is available through a different URL (versionName.latest.appName.appspot.com), and you can choose one of them by default (appName.appspot.com). However, keep in mind that all versions use the same data store and memcache.
So, do not delete the local copy of the application (and, more importantly, its source, if it is a Java application) after deployment.
You can remove the application from App Engine (from Google servers) using the admin console.
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