I upgraded a cluster from 2.4 to 5.6.10 and then from 5.6.10 to 6.3.1. After the upgrade of 5.6.10, I ran the upgrade helper and reindexed all the indices that had originally been created in 2.4 as per the instructions. I queried those indices and all seemed well. Then, after the upgrade from 5.6.10 to 6.3.1, the only index I see is ".kibana".
Is this possibly a security issue? I'm still using the default elastic:changeme username/password and have not created a /etc/elasticsearch/roles.yml file (yet). When I look in the elasticsearch "data" directory, I do see what seems like approximately the correct number of index directories. But a /_cat/indices?v request shows only the ".kibana" index. Help!