How did you eject it? On Windows, you should right-click on the drive letter and select "eject". Don't do a simple "safely remove hardware". The "eject" tells NOOK that it's being disconnected, then tells Windows to disconnect it. The "safely remove hardware" just tells Windows to disconnect the NOOK without letting it know it's being disconnected.
Windows assumes that when you select "safely remove hardware", you're actually going to remove the hardware by unplugging it.
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