RancherOS upgrade converted config files to empty directories

I just upgraded my server hosting rancher/server in combination with nginx for ssl temrination and forwarding to the RancherUI and an external database container. I use the ubuntu console in RancehrOS.

Before the upgrade the server used RancherOS 0.9.1 which I now upgraded to 1.0.1 with sudo ros os upgrade (I did not stop any of the three running services, expecting the upgrade to stop the conainers gracefully). On reboot the connection to the dockerhost (trying to pull the ubuntu console) could not be established twice which led to two further restarts. After the second restart the image pull worked fine and the system could start.

Unfortunately next I could not connect to the rancherUI. I found out that the issue is the persisted config file of the nginx container as well as the ssl key and cert file werde substituted by directories of the same nameā€¦ How is this possible?

To me it seems to be an issue with either the upgrade process from RancherOS 0.9.1 to 1.0.1. or possibly because of the inability to fetch the newer ubuntu-console images on the initial reboot. Any ideas? Every help is greatly appreciated!

I just remembered that only a few directories:


are persisted over restarts and mine /data/config/rancher was none of them. So this was my fault enirely!