just to clarify mate. does your forum work as usual? are your forum threads looking for links in the old directory, or is it just search engines your worried about?
if it's just search engines then i don't know any other way but to wait it out... When search engines index your site again they willl update the link.
There's a Spider Visitor hack on here that can tell you what spiders have visited what park of your site... This would be handy to see what searchengines are reindexing what