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When a VirtualHost is configured to allow a custom VirtualHost include (not on by default) you will see a new directory under your "instance" directory at the same level as your "htdocs" folder.
Within the folder you should see files that are tied to your VirtualHost name.
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The first time the configtest returns "OK", the second time is a bad configuration that would cause the instance to fail if restarted.
Once you're happy with the config you can do a "graceful" to make the change take effect. If you're using phpShell make sure you're using a different instance than the one that you're updating!!! 