@John Hopper: I have exactly the same problem but with books I've converted from EPUB to AZW3. That's very curious because those books should not be synchronized.
Regarding my problem with a specific book, I've determined it's due to ligatures I've added to the text. If I send the same book without ligatures, it works. I can see and open the book. After that, if I load the same book with ligatures, I can't see it in the Kindle, but I can access the book using the BACK arrow. Weird...
I don't know if it's a bug with kindle software or with Calibre.
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