You do not need Handler, just a new IIS rule Rewritethat will conform yourfile.swf?*and rewrite it as yourfile.swf(explicitly without adding querystring).
Something like (not tested):
<configuration>
<system.webServer>
<rewrite>
<rules>
<rule name="strip_querystring" patternSyntax="Wildcard" stopProcessing="true">
<match url="yourfile.swf*" />
<action type="Rewrite" url="yourfile.swf" appendQueryString="false" />
</rule>
</rules>
</rewrite>
</system.webServer>