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Based on the examples provided I'm not sure why _(\w+?)_ and replace with <i>\1</i> won't work for you.
Have you tried enabling 'Italicize common cases' under the Heuristics section of the conversion settings? That feature is supposed to handle this for you automatically. If you have cases where it isn't working you can open a bug with an example file at bugs.calibre-ebook.com.
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