By default, cPanel will rebuild the Apache config file when cPanel runs updates, which is nightly by default. When the Apache config file is rebuilt any manual changes made will be removed as it's overwritten. By running the Apache distiller before rebuilding the Apache config file, manual changes can be saved.
Using SSH to get to the command line, make your changes to the Apache config file.
Run the distiller using the following:
/usr/local/cpanel/bin/apache_conf_distiller --update /usr/local/cpanel/bin/build_apache_conf
This will update the Apache configs default and your changes will not be overwritten.