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I DO think there's a common misconception that using calibre's editor will result in the same changes to markup/css that happens during a calibre conversion. That's unfortunate and needs to be dispelled. The truth is that in opening, manually editing, and saving an epub; calibre's editor will honor your markup, css, and archive structure (errors and all) more than Sigil will (again, that's not a dig at Sigil). You will sacrifice some of that control if you use any of the automatic (fixing/beautifying) features, but that's the case with Sigil (and any other automated processing) as well. *shrug*
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