Im no flash expert
I've used Flash a while back, and I noticed this back on one of the first sync updates. Im afraid that all I was able to to was open the .swf files in flash professional cs5. I could only play the file in the timeline, no modifications were possible. I think you'd need the source files (.fla) in order to re skin or make modifications. im not 100% sure on this, but Id imagine it would be quite a involved process to decompile and not mess up any of the code that makes MFT work.
If you find out anything let us know I am interested in making some graphic mods