The firsts step would be to look into the project and see how the soundfiles are loaded.
Are they in the Library or are they streamed from somewhere outside the shockwave?
Then you could substitute theses soundfiles with your own.
The solution you thought of in your first post might seem easy at first sight but it will get impractibale very fast.
public function MP3Pitch( url: String )
_target = new ByteArray();
_mp3 = new Sound();
_mp3.addEventListener( Event.COMPLETE, complete );
_mp3.load( new URLRequest( url ) );
//in your main fla call
var song:MP3Pitch = new MP3Pitch("mySong.mp3");
//this points at an mp3 file that is in the same directory as your published swf