Hi @wajika,
instead of directly changing the fields.yml you can add additional fields to your mapping via configuring setup.template.append_fields in the apm-server.yml. If you want to enable dynamic for http.request.headers you could configure:
setup.template.append_fields:
- name: http.request.headers
type: group
dynamic: true
Be aware though that a template only gets applied to newly created indices. If the index existed before you changed the template, the changes won't be applied to this index. You can check if the template mapping has been applied by calling GET apm-*transaction/_mapping.