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If you delete an app agent from the Controller UI, as described in Manage App Agents, but do not shut down the JVM that the Java Agent runs on, the Java Agent will reappear in the UI the next time it connects to the Controller. 

To prevent a Java Agent from connecting to the Controller, you need to remove the Java Agent settings from the JVM configuration. This frees the license associated with the agent in the Controller and makes it available for use by another app agent. This topic describes how to uninstall a Java Agent from the JVM configuration. 

To uninstall the Java Agent
  1. Stop the application server on which the Java Agent is configured.
  2. Remove the -javaagent argument in the startup script of the JVM.
  3. Remove any system properties configured for the Java Agent from the startup script of your JVM.
  4. Restart the application server.