Ran into the same situation again on the next node that I no longer wanted to use as a data node. The node has zero shards allocated.
sh-4.2# bin/elasticsearch-node repurpose -v
------------------------------------------------------------------------
WARNING: Elasticsearch MUST be stopped before running this tool.
Obtaining lock for node
Collecting shard data paths
Paths to clean up:
/usr/share/elasticsearch/data/nodes/0/indices/myrWs3pnSmuZwTplN3XKdw/3
Indices affected:
important_index_in_use
Found 1 shards in 1 indices to clean up
Node is being re-purposed as master and no-data. Clean-up of shard data will be performed.
Do you want to proceed?
Confirm [y/N]
(Index is not named "important_index_in_use", but I changed it here in the post.)
This index is in use. Why am I seeing shard data here even though the node has zero allocated shards?