Problem Description
You manually make changes to the configuration files located in /usr/local/nagios/etc/ however you later find that after applying configuration in Core Configuration Manager (CCM) these changes are lost.
Explanation
Nagios XI stores all of it's configurations in a backend database. Whenever you apply configuration in CCM, these configs are pushed down to the flat config files located in /usr/local/nagios/etc/. CCM is not aware of changes made to the flat config files.
If you have a need to update configuration files manually, perhaps pushing them from a third party application, you can use the location /usr/local/nagios/etc/static/ as this folder is not touched by CCM.
More information about this can be found here:
Documentation - Manual Config File Management
Final Thoughts
For any support related questions please visit the Nagios Support Forums at: