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At what stage in your update process do the books disappear from iTunes?
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I don't know. Each time it's happened has been when I first open a calibre session, I connect to iTunes and then there is nothing there. I'm not sure if it is something with the end of the prior session or something about the new session.
I always open calibre via the command line now, so I'll have a debug file if it happens again.
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In calibre|Preferences|Plugins|Device Interface plugins|Apple device interface, do you have the driver disabled (grayed out)?
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Yes. That was in the directions in the calibre + iPad post.
-Marcy