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calibre does not support amzn-* media queries, which are a kindlegen specific kludge. You should never leave such media queries in a final epub.
The way conversion works in calibre, you cannot use different sets for css for the different parts of a single mobi file, as all css processing happens long before the output stage.
You can use different css for creating a mobi6 and an azw3 file separately, using the extra css feature, but not for a joint mobi.
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