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I think you're going to have to copy the files to the PC, import them into a Calibre database, edit the meta data in bulk to set up the shelves, and then transfer books back to the reader. I wouldn't go nuts and copy all that to the reader at once again as it may be slowing operations down. Chances are 32GB of entertainment is more than you'll need at a clip. I have an SDHC card, but haven't even bothered to use it. With over a hundred books on my reader, I've used only a small portion of the built in storage.
Frankly, it's probably a good idea to have your library stored elsewhere and maybe backed up on a PC.
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