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This is a kindle indexer issue, not much calibre can do about it. All calibre does is copy the file to the kindle, the kindle indexer then runs and generates the list of books from the files on the device. I'm guessing one of the books on your kindle is causing he indexer to crash/otherwise misbehave. Sadly there is no way to get diagnostics from the indexer so I cant tell you how to find out which book.
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