Follow the steps below,
- Take the backup of /var/cpanel/userdata
- Run /usr/local/cpanel/bin/userdata_update --reset so that /var/cpanel/userdata can be regenerated.
- Move the required files from new /var/cpanel/userdata to old one.
- Move the old /var/cpanel/userdata back after copying the required files.
- Rebuild Apache conf as /usr/local/cpanel/bin/build_apache_conf
- Restart Apache /etc/init.d/httpd stop ; /etc/init.d/httpd start
Suggested by cPanel :)