Just for the records, in case someone else runs into that…
I had a VM running Docker with Rancher agent. I decided to clone the VM to start another host. The result is that it would register with Rancher as the original host - same ID…
root@docker2:/var/lib# docker logs d0fbaa558ece
INFO: Starting agent for 1E8C605DC66644270C5B
root@docker1:/var/lib# docker logs 4bca13e94cb1
INFO: Starting agent for 1E8C605DC66644270C5B
Solution was to delete /var/lib/rancher to clear the data cached.