you can do some things with your web site inside your flash app but because flash has support for limited html tags and other code that may affect your web site's appearance, you're not likely to find the results satisfactory.
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Well how about this for another option:
Sort of turn the issue around... display Flash inside a Web brower.....You display the entire presentation inside a Web page... which just happens to have your Flash application as part of that Web page. This would give you both FULL Flash interaction as well as FULL HTML interaction.... your Web site could be displayed inside a page with an iframe. That page would provide easy navigation back to the Flash page/application using meta refresh (which retreives a different Web page after a set period of time) and then your Flash could go thru and play for a set time and use setInterval to fire off a request for the Web site page after a certain length of time...
Or something like that... it was not clear when/how you wanted to open your Web site.