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Are you talking about the "SGF Chapter Break"'s vanishing?
If this is the case, they serve to provide temp markers in Sigil, used for splitting a document into multiple (x)html files at a later date. They however use a <hr> tag with some Sigil-specific class adding functionality there. <hr> tags however are just generic horizontal rules, and this special use of them will be ignored in other tools.
A better idea is to just mark up your chapters using <h(1/2/3)> tags and generate the ToC from that (This can be done inside Sigil). If something changes during the conversions - Calibre by default will try to use h tags to rebuild a ToC.
If you are only trying to change your quotation marks to the 'smart' characters, you might consider just using regex to do that within Sigil itself - and as such preserving your existing markup without conversion. Calibre also has a few slight bugs with these smart quotes when they follow certain punctuation characters (emdash and semicolon come to mind).
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