Hello Amit,
geonames allows index settings to be overridden as you have discovered. Configuring the index_settings track parameter overrides the default index settings applied in the track. If you want to set refresh_interval, then you will need to configure all index settings using the full path to the setting:
--track-params='{"index_settings":{ "index.refresh_interval": '${ES_REFRESH_INTERVAL}',"index.number_of_shards": '${ES_NO_OF_SHARDS}',"index.number_of_replicas": '${ES_NO_OF_REPLICAS}'}, "ingest_percentage": 1}'
In addition, each designation of --track-params on the command line overrides the previous. Be sure to set all desired parameters in a single flag. It is recommended to put all parameters in a single .json file, and reference the file in --track-params instead to make things cleaner.