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If you generate the ePUB, you can make the final touch up in Sigil. After all, the ePUB is not ready for publication (as stated in the manual). You can then finalize it. The ePUB can be used for generating the mobi file.
Also, don't forget you can add S&R rules to the corresponding document. If you do, the next time the S&R action will be done and you don't have to do it manually anymore.
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