The net-mgmt/icinga2 adds symbolic links to etc/icinga2/features-enabled during upgrade, overriding the existing server configuration. I see that pkg-plist contains: %%ETCDIR%%/features-enabled/checker.conf %%ETCDIR%%/features-enabled/mainlog.conf %%ETCDIR%%/features-enabled/notification.conf It seems to me that the upgrade process should not touch the features-enabled directory, and only update *.sample files in features-available.
Over to new maintainer
No activity for 2 years. I close here. If there are any questions or problems, feel free to reopen it.