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@Coolmeadow - I get the impression you're saving HTML from Word and importing it into the editor. I suggest you save your Word document in DOCX format and import the DOCX into into the editor. My experience is that Calibre does a better job of converting MS DOCX than its does converting MS HTML.
I don't convert until I have a 'print ready proof' in DOCX. The only ePUB editing I regularly need to do relates to layout of images, front matter titivating, and removal of superfluous metadata. I regard the DOCX files as the 'master' - there's where I'd go to create a second edition.
BR
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