I had the same problem after upgrading from the trial to the free license - I fixed mine by executing "splunk clean all" to wipe the slate clean, it happily reindexed everything and life goes on. In my case,
Splunk > Manager > Licensing had been whining for three months about the trial expiration, which was even causing the free license once installed to have more than the 3 warnings permitted per month. That's probably a bug in 4.2. "splunk clean all" fixed it. I have 300Mb total in logs so a full reindex there and then wasn't going anywhere close to the daily limit.
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