I followed this ( http://blog.deconcept.com/flashobject/ ) to solved the same problem and stored flashobject.js in my_sitea_cccess/javascript/flashobject.js
I call the .js from the template with the regular "eZway" :
<script language="JavaScript" src={"javascript/flashobject.js"|ezdesign}></script>
<div id="flashcontent">
This text is replaced by the Flash movie.
</div>
<script type="text/javascript">
var fo = new FlashObject("/design/plain/images/home_viewer.swf", "home_viewer", "665", "150", "7", "#FFFFFF");
fo.addVariable("diapovar", "{$diaporama}");
fo.write("flashcontent");
</script>
One other thing I was thinking about is that the Microsoft patch will probably also affect flash or quick time movies which are uploaded by a site editor using a standard flash template.
yes, as Microsoft seems to change it's mind daily, it should be good to adapt the .js solution to standard way flash movies are automatically "embed". I think it can be simply done by hacking the embed/flash.tpl.
<script language="JavaScript" src={"javascript/flashobject.js"|ezdesign}></script>
<div id="flashcontent">
This text is replaced by the Flash movie.
</div>
<script type="text/javascript">
var fo = new FlashObject("{concat("content/download/",$attribute.contentobject_id,"/",$attribute.content.contentobject_attribute_id,"/",$attribute.content.original_filename)|ezurl}", "objectid{$object.id}", "{$attribute.content.width}", "{$attribute.content.height}", "7", "#FFFFFF");
fo.addParam("quality", "{$attribute.content.quality}");
fo.addParam("wmode", "transparent");
fo.write("flashcontent");
</script>