Ah, yes, of course. If the css file in a particular epub has its text physically hard-coded with color:black or background-color:white attributes then there are likely to be problems when switching to nightmode. With these epubs it's best to remove all references to colour in the css file and let the reading device handle the colours. You can remove the colour from the css file manually or alternatively there's an option in Calibre to remove colour references during the conversion to epub.
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