Rather than trying to rely on external swf timeline
you could create a bridge to communicate with the externally loaded swf from the main application and control it programmatically.
// set up a variable to communicate with
public var loadedSWFMainTimeline:MovieClip;
//add a function to initialize and communicate with the swf
public function onSWFCompleted(event:Event):void
loadedSWFMainTimeline = mySWF.content;
//call some function to reset or control something.
//or maybe direct it to a frame
loadedSWFMainTimeline5.gotoAndStop( 1 );
<mx:SWFLoader id="mySWF" complete="onSWFCompleted(event);" source="/assets/mySWF.swf" trustContent="true" autoLoad="true"/>
You can now control fuctionality in the external swf.
This will work in a browser or compiled app.