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I've tried running the reindexer but with over 63,000 posts it was taking ages and slowing down the site (at the rate it was going it would take 12+ hours to finish).

I'm sure all the posts are indexed fine to be honest. But I noticed that the qa_words table has about 50,000 rows in total, but 12,400 rows that have titlecount, contentcount, tagcount and tagwordcount all set to 0.

Are those rows safe to delete directly in the database?

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Yes you can empty it, but your ^contentwords table is probably the real culprit.

If you empty ^contentswords your reindexing will probably take just a few miinutes. 

BTW - Reindexing will refill both of these tables.

See this list of tables (needs to be updated) that can be emptied.

 

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Just thought I'd note that not all the tables on that page need to be emptied. Just qa_contentwords, qa_posttags, qa_tagwords, qa_titlewords and qa_words.
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Yes, it should be safe. See the end of qa_db_words_recount(...) in qa-db-recalc.php - does exactly the same thing.

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