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I've had this on occasion as well. I don't have HTML Tidy on, but Pretty Print is.
Because of this (as well as other reasons), I never work on the original file, and before making a significant change have a habit of using Save As so that I have a few copied at different stages, so if it cocks up I can revert back. Once I know the significant change has not had a detrimental effect on the book, I'll save it and delete the extra copies as I now know the file is ok.
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