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After saying no to the automatically fix, I would suggest under the Tools menu, click on Reformat HTML and then Mend and Prettify All HTML Files. Basically, it will attempt to fix the easily fixable errors. This should clean up the error you got from the plugin.
OTOH, it sounds as if this ebook is one of the idiocies where all content is stuffed into a single xhtml file.
And a question that I likely should have asked earlier is the title/author of the book. It's possible that someone could grab a sample and see just how screwed up it is.
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