I have the same problem with 6.5.1 and have a search head and a indexer. I have noticed that if we don't get any hit whitin 15 min the search just stops and search.log reports no data found, however if any data is retrieved within 15 min the search can continue for hours with no problem.
I have not been able to break it down as some search can contine without hits, anyway increasing the batch_wait_after_end at the search head has solved it.
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