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The few times I have had this problem I have traced it to a particular set of steps sideloading from Calibre that had not caused a problem with any Kindle prior to the Paperwhite.
With a few books that had already been sideloaded to my PW, I decided to tweak/edit them. I connected to Calibre, deleted the book(s) from device, and then resent the newer versions and disconnected/ejected from the computer. This resulted in those titles disappearing from the PW and only accessible by doing a search to find them. Simply re-sideloading over an existing book did not work. I have now discovered that whenever I am replacing a title that is already loaded I have to connect to Calibre, delete it, then disconnect from the computer. Then, reconnect, resend the book(s) and again, disconnect. All is then normal.
I haven't a clue why this is but somehow Calibre's data file must become confused.
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