it should do just fine. Pretty much all the formatting should carry over to .mobi format, unless the book you are thinking of does something exotic.
(Although for the pedantically inclined, knowledgeable reader who likes fixing up his own books, the actual code might not look so clean on the inside, but hey, you've got the source EPUB anyway!)
And from what I've googled (
), the Cybook Opus supports EPUB.