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You can choose which formats to send when you're doing a bulk load like that. I don't have calibre open right now (I'm at work), so I'm working entirely from memory here; these instructions might not be exact.
Put the SD card inside your nook, and once it's recognized, connect the nook to calibre.
Highlight all of the books you want to put on the card.
There's a down arrow next to the "send to device" button. If you click that, it'll give you extra options as to how things get sent to the ereader/card. There should be an option that says "send specific format to >." Hovering over that lets you choose whether you're sending those files to the SD card or the device. Once you choose SD card, you should get a pop-up asking you to choose which formats are being sent. Click on the appropriate formats and click OK/Finish.
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