I would not have changed the input format... only the output
...oh. Well it looks like Kibana knows what's best for me and went and changed it back to nanoseconds anyway. This brings me back to my original problem. I have to search on nanoseconds and not milliseconds like I set to be displayed in the Index Pattern. I tried outputting to Logstash so I might be able to mutate the field but then I lose all the nice Dashboards from the Filebeat setup.