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If you're letting iTunes organize your media, you should have a Books folder in your iTunes folder (along with Music, Mobile Applications, etc). Any files you purchase on the desktop will be stored there, and books purchased on the iPad will be copied there when you sync. I'm not sure if iBooks are treated like apps (you can redownload them whenever you want) or Music/Videos (one download unless you get get special dispensation from Customer Service), but I'd guess it's closer to the latter than the former.
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