I issued a nginx -s stop and after that I got this error when trying to reload it.
[error]: invalid PID number "" in "/var/run/nginx.pid"
That /var/run/nginx/pid file is empty atm.
What do I need to do to fix it?
nginx -s reload is only used to tell a running nginx process to reload its config. After a stop, you don't have a running nginx process to send a signal to. Just run nginx (possibly with a -c /path/to/config/file)