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I didn't yet see a ticket on this one, but I had the same problem pop up. I had change Calibre's preferences so that uploads went to the the card under "My Files/My Documents" (the documents were PDF files). I forgot to change it back before uploading some books, and while the Nook sort-of knew they were there, they did not show up in when browsing the library, but did show up when I used the Nook to create a "shelf".
Which leads me to the real thing I wanted to ask about....would it be possible to have Calibre know to load different document types to different locations rather than one location for all files?
roland
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