You should follow incrediblehelp's suggestion to 301 redirect. Don't let your site drop from a 400 page site to a one page site in a search engine's eyes just because all of the old pages cannot be found. It can take time to get large sites reindexed.
You will probably want to 301 redirect the old page locations to the new ones. It's a server configuration issue. That way, visitors that have bookmarked - or those clicking on an older serp listing - are sent to the correct location. Search engines will eventually pick up on the new page locations. At least some of your link power to those old pages will be transferred(I think people are still debating how much, though). It sure helps the robots find those new pages, too.
We compiled some other tips into a blog posting last year:
Web design followup: What to do after the big site launch