In the Kibana indices page, I have changed a seconds Duration field to 00:00:00.[000]. In my dashboards, these values look great. I assume that information is getting saved in ES. Now, I need to export it from ES, so I can import it into another ES instance. I have tried curl with the _mappings keyword, but I do not see any info about the Duration format that I had set in Kibana.
Kibana field formatters are not applied at display time, they do not effect the data stored in Elasticsearch. In order to change the Elasticsearch data you will need to use the _reindex API
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