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The best way to do what you want to do is to use tweak book option in the right click menu. Once you are done editing the html file press rebuild book and you should be able to convert that file. Word is the worst possible app for editing html file. I would recommend using something like notepad++. If you are uncomfortable editing html code then I would recommend using sigil the epub editor instead of messing around with html files and edit the epub directly before converting to mobi.
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