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How to Rebuild Apache Config (httpd.conf) On cPanel VPS SSH Web Host
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Please note that this post is over a year old and may contain outdated information.
Run this command and cPanel will rebuild the Apache httpd.conf file:

/scripts/rebuildhttpdconf

This rebuilds the httpd.conf file from the cPanel templates at /var/cpanel/templates/.

Restart Apache
Your web server will not be affected until you restart Apache, which you can do safely either inside WHM (Web Host Manager):

Restart Services -> HTTP Server (Apache) -> Restart
Or via SSH command:

/scripts/restartsrv_apache