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I would like to revisit this issue rather than submit a duplicate thread. Just to restate the OP's issue in my experience with Calibre 2.82:
Converting to any file format other than DOCX uses the margins set in the Preferences as a starting point. As noted, if the margins are manually changed during a conversion, those changes will be retained if a conversion is performed again (per book basis).
Converting to DOCX appears to bypass the margins set in the Preferences, and 72.0 pt is set for all margins as a starting point. This occurs for both individual book conversions and bulk conversions.
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