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Seems like to you are doing conversion too early. These kinds of things are more easily fixed in a word processor, then when happy with all that then convert and fix the epub bugs.
If you have Word, you can use Toxaris add in to create an epub. Atlantis word processor takes in Word and other files and publishes epubs.
Seems like that might be less work to approach it that way. Sigil was never designed to be the original source of text, though it does remarkably well.
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