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I can't point to any factor that causes the side-loaded material to be corrupted, other than that it happens after ejecting the NOOK from a computer.
I haven't succeeded in explaining the issue to B&N customer service.
One observation: after ejecting the NOOK, the thumbnails of the side-loaded books (both the newly added books AND those previously added) appear in the "New & Recent in My Library" area (top half of the home screen). They ALL seem to appear, flashing by in batches (which can take a few minutes, if you've added a lot of epubs). I suspect that the NOOK (for some reason) is recognizing all the side-loaded books as if they were brand new, which would explain why they don't show up on the previously created shelves.
It might be that interrupting this process messes up the NOOK's memory. Even when the PC tells me that it has safely ejected the NOOK, I try to wait a while before unplugging it. Personally, I wait for the NOOK to go back to its screen saver before unplugging or using it.
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