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Calibre's great strength is that it can convert from almost any format to almost any other format, but it does this by converting all formats to an intermediate internal format and back out. This can and does have an impact (and mainly for the good). But if you want to see the azw3 in as close to original format as possible when converted to an epub (especially as it may have started life as an epub) I would try with KindleUnpack first and only clean it up if it has some difficulties.
That is why kindleunpack was created in the first place. It when used with kindlegen can make epub -> mobi -> epub -> mobi ... tweaking and polishing possible.
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