So is it possible to fix this index now? Can I just delete the most recent segment that was created? I can find this by ls -alt
Sorry, I forgot to answer your question: this should work fine. I don't think you should even have to delete that segment.
Also, to elaborate on my previous comment, a mergeFactor of 5000 not only delays the work until the end, but it also makes the disk workload more seek-dominated, which is not optimal. So I suspect a smaller merge factor, together with a larger minMergeDocs, will be much faster overall, including the final optimize(). Please tell us how it goes.
Doug
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