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Your Kindle is probably stuck trying to index a corrupt or problem book rather than re-indexing all of them.... to check, do a search on a non-sense word like 'ptlrk'. If it still has items that have not been indexed, you will need to start deleting books you've loaded until you find the bad one. (If you reconvert it via Calibre there is a good chance it will index properly). This is not unusual and is a pain. It's generally best to side-load books in small batches rather than one big one so you have an easier time troubleshooting the problem book.
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