Hello,
I was testing on commmit Ian sent to reproduce, and now moved to newest guix, seems to have been solved (at least the specific error I was getting), possibly by shepherd 1.0.3 update. With newest guix both the first reconfigure of guix system image and subsequent ones are fine. Let me know if you're still experiencing this issue after updating and I might try harder to reproduce if I got a different issue on first try. I am afraid this will be hard to debug on real hw as you don't really get the log in /var/log/messages for shutting down the system, I had to get it through a serial line via stdout of qemu. Also I was able to reproduce the issue on the older guix just by running the shepherd services upgrade scm script, no need for full reconfigure, this shows that something has gone wrong when shepherd was reloading the services. Do we have some kind of a test for this in guix / shepherd so it can't happen anymore in the future?