You can remove an application instance, so that it no longer takes part in your Applications Links suite.
Click 'Remove' next to the relevant application instance.
If there are no existing project links associated with the application instance, it will be removed from the Application Links suite immediately. For more information about project links, refer to Adding and Synchronising Project Links via JIRA.
However, if there are existing project links associated with the application instance, then you will be asked whether you want those links deleted or reassigned to the default instance. If there is no default instance, and you choose to reassign the links, they will automatically be assigned to the new default instance when one is created.