***UPDATE... AGAIN***
Okay so I think I have the real answer to your question here. Check out this documentation:
http://livedocs.adobe.com/flex/3/html/help.html?content=19_External_Interface_10.html
You'll want to use the axShockwaveFlash.FlashCall interface.
***UPDATE***
Found this link:
Get instance of Excel application with C# by Handle
Explains how to fetch a reference to an active application instance.
***ORIGINAL POST***
I agree with alxx this is something you'll have to do natively and I don't know that it will be all that easy to do. You'll have to grab the flash instance somehow, and I'm not sure how difficult that is going to be there are a lot of variables at play to account for. However, I can say it is possible to do and here is some documentation on how to do this with various languages (C#, VC++ etc):
http://msdn.microsoft.com/en-us/library/ms171548.aspx
And here is a blog post of mine on how to interface with the flash control in C# (at least to give you an idea):
http://blog.ascensionsystems.ca/?p=153
There is a link to the source code as well available on SVN. This isn't the greatest answer in that I'm not offering any exact method but I hope this is a good start for you.