Docker services are not long running processes on a base OS. The entire OS is pretty much freshly created when you spawn a container. This gets to be an issue with letsencrypt.
What we do is take a 3 year certificate and bake it into docker build. So we only have to mess with it very infrequently. I can shutdown and scale my nginx containers (meaning - spawn new ones). Since the certificate is baked into the VM, it works seamlessly.