About the two processes: This is probably caused by the init script in combination with shutdown_timeout. It only kills filebeat-god and does not wait long enough for filebeat to also completely shutdown when shutdown_timeout is used. This leads to 2 instances writing / reading from the same registry file which is not good at all, especially on startup 
Any chance you could test to restart filebeat without the init script and see if the behaviour persists? It would be nice if we could have something like TimeoutStopSec= in systemd for these init scripts, unfortunately each platform is a little bit different.