It is not recommended to clone the indexers configurations by copying the whole $SPLUNK_HOME directory. We suggest you to instal Splunk software package and have deployment server to distribute configurations to indexers. As just copying the whole directory image, the indexer's GUID will all be the same and it will cause some unexpected behaviour.
If you have used copying files to clone indexer's image, you can use the below command and generate another GUID.
./splunk clone-prep-clear-config
