Issue :
The apache configuration file (httpd.conf) has several custom entries which should not be over-written when an EasyApache is done for recompiling/adding a PHP/Apache extension.
Solution :
Starting with cPanel 11.x, all the apache settings are also stored in a database and the configuration files are recreated each time an account is added or a recompile is done.
To also save the changes in the database you will have to run:
/usr/local/cpanel/bin/apache_conf_distiller –update
You can check to see if the changes were accepted and will not be discarded at the next apache recompile by running :
/usr/local/cpanel/bin/build_apache_conf