Ok, Not sure whats happening. So do you have have schedule task or cron job copy the directories/files over? Are you using CRCsalt? Install SOS (Splunk on Splunk) App or search the _internal index for the source which may give you some ideas.
Considerchanging your File checksum configuration to [endpoint_md5|entire_md5|modtime] in your props.conf.
If no luck up your logging channels on your indexer (I am not familar with all the logging channels):
FileInputTracker
FileTracker
recordFileManager
WatchedFile
Also keep in mind that Splunk indexes its own logs as well as those from your Forwarders which is stored in the _internal index. _internal does not count against your license.
Hope this helps or gets you started.
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