The continuous deployment system doesn't know how to deploy changes that require a system reboot
The continuous deployment system eventually runs morph deploy .. switch --on <target>
on each managed host, with each host targeting itself.
If there are changes to deploy that don't take effect until a reboot, the deployment management system will never arrange for the reboot to happen. Thus, they will never be deployed automatically. An admin can manually reboot the systems and re-upload secrets to cause them to be deployed.
It would be nice if this part of the deployment process were also automated by the continuous deployment system.