Here is the answer provided by support. I verified the solution is good. Ambari has template files that overwrite the nagios cfg files when the service is started by web interface. The typical location of the file that needs to be udpated by the root user is. /var/lib/ambari-agent/puppet/modules/hdp-nagios/templates/nagios.cfg.erb. Once these are updated you can stop and restart the Nagios server with the customizations in place. One item of note is the ambari stop/start does not utilize cache files.