This bug has happened to me several times. After I send books to my Kindle Touch (using Calibre), it shows on my device and in Calibre that the books are on my device. However, if I shut down my device (and turn it back on again), the books will be missing (i.e. not showing). It still shows in Calibre that the books are on my device but the books do not display in my Kindle. The only thing that fixes this it is to revert to a previous state (via a previous backup).
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P.S. Sorry if this is the wrong forum to discuss this in, but the support guy here:
https://bugs.launchpad.net/calibre/+bug/900782 sent me here.
P.P.S. More details if required.