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Have you checked the ePub to see if there are any color codes in the CSS? That could be the problem. If you have the text color set and set to black, then when you go into night mode, you'd have black on black. Look at the CSS of the ePub and if there are any color codes, remove them and try the conversion again. If you don't see any color codes in the CSS, look in all the XML files to see if any color codes are there.
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