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I manage my library in Calibre and I trust my online retailers to save copies for me.
My library is on a portable external hard drive and if I want to re-read a book, I copy the epub over to either Dropbox or iTunes on my computer's internal hard drive --that would be my backup of the books most important to me.
(I should add that I download books to my computer and I leave them there after I import them into Calibre; I otherwise do not do anything in particular to preserve them. They fall under whatever back up strategy I use on my computer, but they are "raw downloads" and not "cleaned". In theory, I could go back to them if I needed to, but am not concerned with them.)
Of all the digital media I keep, books are low on my priority list, so I do minimal management of them.
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