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I have a similar issue in that, since the 0.7.12 update, Calibre has reversed my memory card and main memory. In other words, my 4Gb external card appears as the main memory and the internal 2Gb card shows as the Card A. I removed the memory card and added books to my Main Memory (which was fine with no SD card present). they added correctly to the My Documents folder. When I added my SD card back and restarted Calibre, the files I put on main memory now show as being in Card A. The bad thing is that when it thinks my main memory is th external card, any new books I put in there do not go into My Documents but just to the root drive of the nook. MY nook is showing as drive F: and my external card is showing as drive G: both in my PC and in Calibre. So that is correct but Calibre insists on recognizing the G: drive as the main drive.
I noticed that my PC also notices the external card before recognizing the nook, and I suppose that's why this is happening. I read of a similar instance but it was fixed with an earlier version of Calibre. Somehow it's crept back...at least for some.
I'm sure this will get fixed by the next release as the developer is great about taking care of and fixing anything like this...I just wish it was sooner as I miss my Calibre and I only added a few books to get me started. A week will seem like an eternity.
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