I was thinking about exporting the ePub, renaming it as a ZIP, then reimporting it into the book and converting to ePub. You might want to store the ePub somewhere safe externally, as it is going to be overwritten.
As for the chapter order, there's a
FAQ entry relevant to file ordering in multi-HTML books. I should have a small script still floating around for creating the index file discussed in that FAQ entry that I hacked together once for the purpose of converting a HTML reference book, but it only cares about what the first file is and dumps the rest of the files in as it finds them. Still, should that be useful, I can post it here.