After discussion between Infinispan and Keycloak team regarding indices and re-indexing, it turned out there is currently the only one "supported" way how to change an index:

1. Remove the index files on disk
2. Start the servers and run the mass-indexer

This requires downtime which we are trying to avoid in the new Keycloak storage. It would be great if there is a way how to do it without a downtime.