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Coming late to this thread, but the advice about heading styles is spot on. In my experience the biggest mistake people make when creating EPUBs from Word is skipping proper styles — they manually bold and enlarge chapter titles instead of using Heading 1 and Heading 2. That one habit change alone gives you a proper table of contents and chapter breaks after Calibre conversion with zero extra effort. For cleanup afterwards, Sigil with its live preview and regex find-and-replace is the most efficient workflow I've found for fixing the formatting quirks Word leaves behind.
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