If you just want to prompt user to save the file in local system, you can try FileReference
for that.
like :
file = new FileReference();
file.addEventListener(Event.COMPLETE, completeHandler);
file.addEventListener(IOErrorEvent.IO_ERROR, errorHandler);
file.save(mc, "myMovieClip");
here mc is any type of data you can provide, in your case you can provide your dynamically generated PDF file, and "myMovieClip" is name which you wan to give that file.
try this, might be useful for you.