Zpanel keeps it's control panel and client configurations in the same file
/etc/zpanel/configs/apache/httpd-vhosts.conf. When changes are made to any of the panel's domains, this file is automatically updated. This overwrites any changes to the panel's vhost config as well.
To avoid having your SSL vhost config continuously overwritten, you must put it in a separate file and have it sourced by adding an
Include directive into the primary apache config file
As an added bonus, adding encryption to the control panel will in turn encrypt the webmail, phpmyadmin and any other pages accessible from the panel.