Why can't you make the corrections in the HTML version? Use an editor such as notepad, vi (command-line), etc., and correct the HTML. If you correct the Word version, it is possible that the HTML problem will persist, as the Word version has to be converted to HTML again to become a .mobi or whatever file.
I've not done it in Word, but in OpenOffice, I can edit an HTML file, and save it as HTML. Maybe you can do the same in Word? The doc will appear formatted and everything, so you can see what you are doing.
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