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You are expecting Calibre to know what you want to do with your poor source. Well, it's not always possible to know what to do and thus, you have to take responsibility that your source is good enough. Given that you are going to ePub, just buck it up, and fix up the ePub after it's done. It's very easy to fix the indents. If you don't know what t do, be nice about it, say you don't know what to do and then you can get help.
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