Bots don't read javascript so, have your flash site wrapped in a div, then redo all of the content on the flash site in standard html and wrap that in a div.
The javascript below will detect if you have a flash player if you do, you get the flash version. If you don't you get the html version. This also solves the problem with iphones, really old browsers and people who don't want flash installed.
I wrapped it all in jQuery so you can make the non flash site look just as good. The only problem with this is if some one has javascript turned off gets both versions. Oh well, think SEO is more important then people scared of javascript.
<head>
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.7.2/jquery-ui.min.js"></script>
<script language="javascript" type="text/javascript">
$(document).ready(function() {
if ((navigator.appName == "Microsoft Internet Explorer" &&
navigator.appVersion.indexOf("Mac") == -1 && navigator.appVersion.indexOf("3.1") == -1) ||
(navigator.plugins && navigator.plugins["Shockwave Flash"])
|| navigator.plugins["Shockwave Flash 2.0"]){
$("#contentWrapper").hide();
}
else {
$("#flashWrapper").hide();
}
});
</SCRIPT>
<title>Searchable flash site</title>
</head>
<body>
<div id="flashWrapper"></div>
<div id="contentWrapper"></div>
</body>
</html>