When cPanel is updated or Httpd service is restarted using WHM, the custom changes made in the Apache configuration file directly won't work because cPanel looks the new values in the file /var/cpanel/conf/apache/local.
However, you can still make the changes directly in the Apache configuration and run the following distiller commands to save the changes. In order to make the changes permanent and make sure the changes don't get overwritten on the next cPanel update / WHM restart, execute the following commands:
# /usr/local/cpanel/bin/apache_conf_distiller –update –main
# /scripts/restartsrv httpd