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As soon as you switch between code- and bookview, Sigil must make choices and guesses. Although in this case I think there usually is just a warning, but there were several issues with this in the past. I have lost content as well in the past, but that was on 0.4.2 or something like that.
Use the preview for looking how things look. If there is an error in the code, it will say so without changing the code. Myself I have the preview docked on the right side (switchable with the TOC). I never go to bookview anymore.
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