Use an swf decompiler?
Using an swf decompiler you can make an FLA file of an existing swf file and edit it. In most cases I found it to work very well. Look for Sothink swf decompiler, there might be others as well. After decompiling it's easy to find the page url's and edit them, compile using Flash and there you are. Hope this helps.
I ended up just doing it the easy but maybe not very sophisticated way.
Basically, what I did was leave all the flash pages on the site root, rename the flash home page that was index.html to index.htm, create a new html page and name it index.html and include a link to the flash version at the top of the new index page. So basically now if someone goes to the site they see the html home page as required, and have the option to choose the flash site. If they choose flash, they can navigate between all flash pages as usual EXCEPT that if they click the link back to home they end up on the new index.html page and get dumped back into html. It was the only way I could come up with to handle this situation. Not the best or prettiest or smoothest, but the client is happy.