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Make sure the Heading paragraph style in Writer has no list property, only heading level, and only for headings you want in TOC.
Edit only odt, but do an extra Save as docx. Only add docx to Calibre. Never edit a "Save As" docx from Writer in Writer as it reconverts it!
I'm on 6.4.7.2 on main PC, though I have newer version somewhere else, and I don't get headings as list. I guess you are ading an odt to Calibre, which doesn't work so well.
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