OK - I have figured it out. To load up the modified fields.yml file into the template, you need to run the filebeat module that is generated, as the index template is part of the filebeat module (why is that not separate to the main executable!) and does not use the fields.yml file at all. I also could not find the filebeat.template.yml file that is mentioned elsewere in the discuss forum so I gather this was deprecated in v6 or v7 beats? So, my understanding, to create a filebeat module, which has fields not already defined in the template (ie you have custom fields), requires that you compile a separate standalone instance of Filebeat and potentially run that, or use it to export the template. That to me is just ridiculous. Filebeat should be the engine, and the template it loads, same as the modules should be separate to the engine and not part of it.
So, from what I read here: Where is the default template.json file for filebeat - #3 by Daud_Ahmed you need to export the template - and load it up into Elastic, and then rinse/repeat for each filebeat module that you deploy to the environment in the future that requires those additional fields. This sounds like a nightmare if you have different modules across the environment. I gather component templates might fix this - haven't got my head into this.
Can someone update documents somewhere about this (it may be there but I did not come across it)