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Please Ignore the below as DiapDealer has already fixed the issue in Sigil 0.9.8 which is why I could not recreate it in master.
Turtle91,
On a copy of the problem file, would you please run Sigil->Tools->Reformat HTML-> "Mend All HTML Files" just **before** trying your problem merge and let me know if the issue goes away.
That way we can rule out non-well-formed xhtml from causing the problem.
Please let us know what you see.
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