Please note that this post is over a year old and may contain outdated information.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:
This rebuilds the httpd.conf file from the cPanel templates at /var/cpanel/templates/.
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: