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You have encountered why some prefer to not use Calibre. It works, but the resulting code can be hard to understand.
This is a reason to get acquainted with regular expressions. You put <whatever calibre tag>(.+?)</whatever calibre tag> in find. You put <i>\1</i> in replace. Set the search for regex. That should get you just the expressions and replace them with ordinary italic tags.
Test this out by finding just one, then press replace. You should see it change to what you want. Then you can do find/replace repeatedly and when you get brave replace all. Even though calibre can take you back, do a save before you do anything with replace alls, just in case.
Or you use AWP or fight with Toxaris' add on until you get it to work. They don't add all the extra stuff.
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