I've this configuration in a test environment :
1 SEARCH HEAD < (dist. search) > 1 INDEXER (no clustered environment)
I set up indexes on the indexer then I still added those (dummy) indexes on the search head for management reasons.
The problem is with the Splunk Add-on for Java Management Extensions (JMX) : it's still writing on the local index of the search head! How to tell it to write on the indexer instead?
did you configured your Search Head to forward its logs to the Indexer?
After you can see to your Add-On to send logs the index you want.
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Splunk internal logs are stored in _internal index.
When Splunk doesn't find an index, it puts logs in index=main.
Every way, try this search
index=* sourcetype=yoursourcetype and verify if you have logs and in which index.