Yes, having something be above the content.opf (in a higher directory) has probably never been tested. I have seen equal and of course in subdirectories but I don't think I have ever seen one where you go up a directory from the opf. That said, the way we build up the absolute url from the relative should properly handle this case unless the filenames don't match exactly in case.
I will try to look at this today if I get some free time.
KevinH
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