Rancher 2.x uses etcd to store everything. If you don't know how to backup that, you loose all info on clusters, etc. as you upgrade Rancher Server.
Here's how to get passed that!
Get container ID:
$ docker ps|grep rancher/rancher
Create directory on host (because next time we will mount this):
$ mkdir /opt/your-org/
Copy files from container:
$ docker cp CONTAINER_ID:/var/lib/rancher /opt/your-org/
Restart Rancher Server:
$ docker run -d --restart=unless-stopped -p 80:80 -p 443:443 \
-v /opt/your-org/rancher:/var/lib/rancher rancher/rancher:stable \
--acme-domain rancher.your.org
Now backup /opt/your-org/
regulary and you are fine!