Zabbix server has been installed to Ubuntu computer using apt method from Zabbix official repository. When the server is upgraded using the "apt-get upgrade", configuration file gets usually overwritten. Please see as follows:

Setting up zabbix-server-mysql (1:4.0.6-1+xenial) ...

Configuration file '/etc/zabbix/zabbix_server.conf'
==> Modified (by you or by a script) since installation.
==> Package distributor has shipped an updated version.
What would you like to do about it ? Your options are:
Y or I : install the package maintainer's version
N or O : keep your currently-installed version
D : show the differences between the versions
Z : start a shell to examine the situation
The default action is to keep your current version.

• • • zabbix_server.conf (Y/I/N/O/D/Z) [default=N] ? y
      Installing new version of config file /etc/zabbix/zabbix_server.conf ...

As I remember, the same problem is also on zabbix-proxy.

This should be corrected by using the same method in zabbix-agent i.e. creating a directory for local configuration and letting the local configuration to override values set in the distribution configuration file. Here is cut and paste from zabbix-agent configuration file - similar mechanism should be introduced to zabbix-server (and zabbix-proxy) as well.

1. 1. 1. Option: Include
2. You may include individual files or all files in a directory in the configuration file.
3. Installing Zabbix will create include directory in /usr/local/etc, unless modified during the compile time.
   #
4. Mandatory: no
5. Default:
6. Include=

Include=/etc/zabbix/zabbix_agentd.d/*.conf

1. Include=/usr/local/etc/zabbix_agentd.userparams.conf
2. Include=/usr/local/etc/zabbix_agentd.conf.d/
3. Include=/usr/local/etc/zabbix_agentd.conf.d/*.conf