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I'd get out the big sledge hammer and delete those spans from the epub. You can open the epub in Sigil and it has a plugin called TagMechanic (both of which you can download from here) and in TagMechanic you can specify a tag and its class to delete. Remember in the book list on the left to select all of the files/chapters you want the plugin to modify. I use it all the time for junk like that, e.g, spans for a drop cap, useless divs, etc.
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