I've had the same thing happen, but only with one author's books, and not all of them. Two of the first three of L.E. Modesitt's Imager books would appear and disappear on the Kindle. If you didn't see them, when you plugged the Kindle in and accessed Calibre, Calibre would show them on the Kindle, and when you unplugged the Kindle, there they were. But the next time you plugged in with Calibre running, the books would disappear. But they would appear again the next time you plugged the Kindle in and accessed Calibre. I finally just sideloaded them in the documents folder and they remain on the Kindle.
Jim
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