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Hmm ... that has never happened to me. In Sigil Preferences try enabling Mend on Open just in case there is an issue with not well-formed xhtml or errors in the opf. If that doesn't help, then I would guess the issue is something in that particular epub confuses Sigil for some reason.
If so, I would appreciate you posting the problem epub privately someplace and PM ing KevinH (me) or DiapDealer (the developers/maintainers of Sigil) on this MR site with the url of the epub you posted.
We will be able to debug what is causing the problems for Sigil and let you know how to workaround it until we get that bug fixed. Once we have the problem diagnosed and fixed we will delete your problem epub from our machines.
Please do NOT post it publicly unless you are the author/copyright owner.
Thanks for your bug report.
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