While upgrading ispconfig from 3.1.2 to 3.1.3 /etc/bind/name.conf.options was overwritten with a default configuration, removing all of my changes, is this intentional and will it reoccur or was it a one off? I am using debian 8
That's intended, ISPConfig has to update config files during update. If you do not make your changes update safe, then they will get removed. Copy the file install/tpl/named.conf.options.master from ispconfig tar.gz to the folder /usr/local/ispconfig/server/conf-custom/install/ and implement your changes in that file to make them update safe.
