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If you ever get an error about a tag not closed, etc., do you ever tell Sigil to fix it automatically? I never do and I've never experienced what you're getting.
When I'm doing major changes to a book, I often make a copy of the epub so if I screw something up badly, I still have the full version of the untouched book to recover. Until you sort out why this is happening, I'd suggest always making a copy before you start editing again.
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