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You did not do the conversion the best possibly way. The best way to go from AZW3 > ePub is not by converting at all. The way to do it is to install the KindleUnpack plugin and use that to shift the AZW3 files to an ePub. Then you can use Modify ePub to fix the cover. After that, you can use Sigil to fix anything that's not structurally correct with the ePub and make any other changes you want.
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