Hi ropc,
Thanks for your reply, this was really helpful!
I'm not sure how meta.json could have been the same - I don't think we are deploying anything there but am looking into it.
However I tried deleting the meta.json and straightaway it generated unique UUIDs for each host. Both UUIDs are now showing up in the .monitoring-beats index, but not in the UI which is interesting. I have about 15 minutes of data so far, but even with the monitoring UI set to 5 minutes I don't see anything.
I'll send you the case number in a PM.
Thanks again!