When you delete a secondary site, this action deletes information about the secondary site and its resources from the Configuration ...

When you delete a secondary site, this action deletes information about the secondary site and its resources from the Configuration Manager hierarchy and leaves Configuration Manager installed on the secondary site server. Use this option if one of the following conditions is true:
        -  A site has failed to install.
        -  The site remains visible in the Configuration Manager console after you have uninstalled it.