Keep in mind that more than one instance will not help you if they should use the same input. Except you are able to send your netflow events to different ports per instance. I have also a performanceissue with filebeat and netflow, see here: Performanceissue with Filebeat and Netflow Input
May I ask you how much Events are you able to send through filebeat? In my case it's ~20.000 flows per second, I have to add an additional VM to get 20.000 more which is not a solution. Somehow it must be possible to get better performance with a single filebeat instance.