I finally got the books to all index!
Reading on another forum, I found that holding the sleep switch for about 20 seconds resets the Kindle. I copied all the files on the Kindle to my computer and then deleted them on the Kindle, this might not have been necessary. Then I reset the Kindle and put all of the books back on. The books started indexing immediately and (I did this last night) now they are all indexed.
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