Did you ever find any any additional information on this?
I have a similar issue. I can update the document manually with the update api call but using the Logstash Output has the same issue you listed here. The new fields are mapped correctly but its not displayed. I have also tried the "update" action.
The additional fields were being added correctly using the aggregate function but I had a mutate method that was removing the fields after formatting. Once that was resolved, the records and new fields were being updated as normal.
Both the default insert action and update action worked for the Elasticsearch output method.
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