My shelves are still there. It sounds like you guys are running up on the micro SD card shelving issue and I would LOVE if B&N would fix the damn thing!
Basically if you reboot, sometimes if you connect your nook to a PC and also if you update the firmware, all books shelved from a micro SD card will disappear from your shelves.
Content from the built in storage pool and books from B&N that are loaded in the B&N reserved space are preserved on your shelves through reboots, firmware updates, etc. Or at least that has been my experience.
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