A really simple fix is to leave an index.html in place where everyones' bookmarks will find it, and then use a very simple redirect to your new site's mainpage.
<html>
<head>
<script language="JavaScript" type="text/JavaScript">
<!--
window.location = "new url"
//-->
</script>
</head>
<html>
The worst anyone is going to see in their browser is a blank page flash for < 1 sec before the new main page loads. Usually it's seamless if they are on the same host.
[/code]
There are umpteen ways to redirect, but I found this little bit of code to be very reliable in any environment.