The first thing I'd try is one of the file recovery programs you get with high-end CF cards, like the Lexar UDMA 300x ones. If it won't see it, then I'd try
Disk Warrior -- that's fixed this kind of problem more than anything. I've been using it for more than 10 years and nothing comes close to fixing disk directory issues (which is what this sounds like).
I try to run it at least once a month on all the hard drives to keep them in good order.