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What iBooks is doing is unzipping the .epub file into a folder structure whose name comes from an id assigned by iTunes/iBooks (the strange sequence you're seeing).
I agree it would be nice if Apple would make it possible for 3rd party apps to add and delete books into iBooks. For readers who do find it useful to be able see what books are installed on their iDevice from calibre, Marvin is the best alternative at this time.
G
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