Loosing some data is expected hind sight being 20/20 you probably should have backed-up some data, myself before upgrading I actually tried reseting the device as close to default as possible using the 'clean state' and 'format internal memory'.
Could you try removing those books from the device and transferring a new copy ? if that doesn't solve it maybe we can learn more about the problem, I've only seen that bug that I mentioned up top about adobeviewer and its not new to this version.
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