HomeKit devices lost room assignments and automations after HA upgrade

I use HomeKit for my primary smart home functionality, and HA as a way to add additional functionality into HomeKit. I recently updated HA to version 0.90.0. After doing so, my HA HomeKit devices lost their room assignments. But worse, all of the HomeKit automations that were build using HA devices were lost or mucked up. Am I doing something wrong? Does anyone know of a way to prevent this from happening next time I update HA?