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One thing that I would recommend is to provide a non-Flash "escape hatch" of text links that still allow you to traverse the site without going into the Flash pages. Or you can add text links on HTML pages that have Flash (e.g. a static text "skip intro" link that bypasses the Flash). That will help with any search engine bots that don't know how to crawl Flash .swf files..
My rule of thumb is "make sure that you can reach any page with a static text link." Usually that boils down to something like a site map, but that simple rule of thumb is probably what I end up recommending for 90% of sites that have problems with crawl coverage.
Good luck and let us know what you decide to do.. :)