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I have two books that are essentially zipped up HTML files. The structure is that there's one file in the root, everything else is in subfolders. They convert OK (at least, the part up to ePub generation, where it chokes horribly, I suspect that's because the HTML is so full of crap that I lost all hope of correcting it, together with the fact that each of the two books includes some 20.000 files). Did you try just hitting convert and see what happens?
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