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Don't know about the second problem, but as to the first, I suspect:
1. It used a lot of juice indexing the new books.
2. Leaving auto-rotation on can drain the battery faster, but you seem to imply it was just laying there while you slept, not jostling around in a bag while you were moving. (Still, they say it can drain the battery just by being on, though I have not noticed anything so dramatic as what you describe.)
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