Moved over from a bare metal Ubuntu/Raid5/TVHeadend setup and I've been using your plugin for TVH but I've hit the same issues noted here with the config seemly being lost after a reboot (or is it a array stop/start?)
Did you make any inroads to the issue? for now, I've made a backup of the /usr/local/tvheadend/.htsconfig which I copy back if the config reverts.