Cpanel have consolidated all management of httpd.conf into a "cPanel" database, found in /var/cpanel/useradata. The script apache_conf_distiller is used to create and maintain that data. httpd.conf is rebuilt based upon that data. You will have to make changes there before running apache_conf_distiller. Best option is not to run this script.
Just restart apache after making any changes to apache conf.
I don't recommend you to modifying the data in /var/cpanel/userdata if you don't have a good knowledge in cpanel.
Cpanel have consolidated all management of httpd.conf into a "cPanel" database
If you're going to comment on something, make sure you know what you're talking about. The specific directory has nothing to do with 'apache', but with cPanel, and users. This will not affect apache at all.
Depending on what you're trying to do, there are various alternatives to try.
If you're trying to modify a user's directives (ie: add additional domains, etc), httpd.conf has directions for you to follow.
If you're just trying to add directives to global apache configuration (ie: I maintain a copy of phpmyadmin for my access, etc), then you can simply add those directives to conf/includes/pre_main_global.conf . Here's how I have mine setup
Alias /phpmy/ /home/phpmy/
Alias /phpmy /home/phpmy/
#get rid of mailman - PCI
Alias /mailman/ /usr/local/apache/htdocs/
Alias /mailman /usr/local/apache/htdocs/
#deny calls to certain filetypes
<Files ~ ".(pl|tpl|inc)$">
Deny from all
I've run into the same problem you have with distiller not saving things properly, sadly. This is one of the main problems I have with cPanel any more, they start to think they can do everything and end up giving themselves too much power.
WHMCS Guru - WHMCS addons, management, support and more. WHMCS Notifications Extended - Add slack, hipchat, SMS, pushover to WHMCS !!
Linux Problems? WHMCS Issues? +1-866-546-8914 (linux-14) or @whmcsguru on twitter!