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You need to get it so there is only one active Elasticsearch index. Talking to ES via its API is actually refreshingly straightforward. By CURLing a command at the local ES port (9200 as of this writing), you can tell it to delete any indexes you don't want anymore, for example:
curl -X POST "localhost:9200/_aliases" -H 'Content-Type: application/json' -d' { "actions" : [ { "remove_index": { "index": "hypothesis-xxxxxxxx" } } ] } 'Lest forming that CURL seem onerous, take a visit to ES' very helpful docs page on the API, which includes the ability to copy pre-formatted CURL commands to your clipboard! Handy.