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If you want to remove an entire directory, you can exclude that directory in robots.txt, then go to Google Webmaster Tools and request a URL removal. You'll have an option to remove an entire directory there.

It depends on how long it will be before the new content is up -if it's a couple days, might as well leave it.  If it's weeks or longer, it's best to change them, though honestly making the change one way or another at this point is not necessarily going to move the site in any significant way - it's difficult to judge how much, if at all.