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It is common for books converted to Kindle formats via calibre to include metadata indicating that the book was obtained from Amazon (CDETYPE=EBOK) as opposed to being a personal document.
Amazon keeps track of which purchased or borrowed books are supposed to be present on each device registered to a user.
It is possible that a cleanup process has been added that is occasionally checking device contents against the user's purchases and removing supposedly purchased books that should not be present on the device.
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