The /var/run/nginx.pid mysteriously disappears after I run "certbot --nginx renew". I can no longer restart nginx manually using /etc/init.d/nginx afterwards. Something fishy is there.
Not a temporary problem, because nginx process is still running after certbot operation, I just cannot kill it using the normal init script, as there's no PID file. I can only kill it with 'kill -9 nginx'.
Checking your domain you have a lot of older certificates.
In my Let's Encrypt configuration I have just a single certificate for this domain, configuration for which I have sent you earlier today.