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As Rudix said, you could also have XOOPS in a different directory. I have my own misgivings about not having XOOPS in the root directory, however.
Either way, your index.html or index.htm file with the Flash code would either have a link (click to enter our site) or a timeout that goes to the index.php --which is always the XOOPS main entry point.
So, the simple thing is to have a very short index.htm that starts with the flash code and ends with a graphic or text link, "ENTER" or whatever, that is a simple link to "http://www.yoursite/index.php" or "http://www.yoursite/xoops/" if you want to put XOOPS in a different directory.
If you want a timeout that automatically loads XOOPS after a few seconds, then it would be best to edit the Flash code to go to your XOOPS main page after the Flash plays.