when calibre converts an ebook, it consolidates all css into unique "calibre*" tags. That was Kovid's design decision, for better or worse. There is no way to get around it by converting, so as mrmikel said, use the editor -- it can edit azw3 as well as EPUB. Or you can use kindlegen.
Is it really a problem though? I assume EPUB will be your master format, what does it matter what the AZW3 looks like inside? You will always be editing the EPUB.
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