I'll answer the root to your question: "I am trying to figure out if I can bring a file with actionscript into After Effects?"
No. When flash exports a video, it exports the literal frame by frame animation of the timeline, no execution of scripts, not even any movie clips on stage actually play like they would in a running swf. This is because video is not a running program, just literally video, frame by frame of what pixels should show what colors.
That's probably why you are getting a blank video, did "moving a couple frames around" involve reducing the Main Timeline to not having any real part in the animation, maybe relying more on movieclips playing? Because then you'd definitely just get a blank video.
If you want scripted animation caught as video then the best thing to do is learn the After Effects based scripting, I believe it is called Expressions, and it is based on Javascript (much like AS2 is). If you want an actual flash file's scripted animation then you will have to capture it as it plays on screen, using software such as Camtasia.