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Kindle is using a much leaner general database but actually stores a lot of info in separate files next to the books. That way, even of the database needs to be rebuilt essentially nothing of value to the user disappears (reading times stats and search indices, but they are easily rebuilt). Another plus: syncs can be almost instantaneous and do not depend on one big process.
Of course the files have to be loaded individually upon opening the book, yet their OS is faster, more responsive and still more reliable.
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