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(I've never heard of Kitaboo, either!)
>I want to get this to work in apple iBooks or adobe digital editions.
But if that's the case, why do you want to turn it into a PDF?
I don't understand how a folder or directory can be an "epub file." If it is an epub file, or files, surely it would open in ADE?
Perhaps you should first open that epub file or files in Sigil, and see if it really is an epub.
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