Cpanel is a great control panel. However, one drawback is that configuration changes and/or customizations are often overwritten after every upgrade. In order to stop cpanel from overwriting your configuration files you must use the following file:
vi /etc/cpanelsync.exclude
The format for this file is one file per line. i.e.
/etc/exim.conf
Then save the file and restart cpanel. This will ensure cpanel doesn’t overwrite the /etc/exim.conf file the next time it processes an upgrade. Now the only trick is figuring out how to stop it from overwriting:
/etc/cpanelsync.exclude
Just Kidding. Give it a try and let us know how this fix works for you.