client side f4f fragment files can only contain four types of boxes (abst, asrt, afrt, mdat). i have never looked at server side f4f files so i can't be sure how hard or easy it will be to demux them. probably you can upload some small sample somewhere. there was some talk on ffmpeg irc channel few days ago about implementing servers side f4f processing. you can give it a shot at their irc channel. also you are using the paid professional product of adobe. why don't you kick the balls of their support team for having ridiculous limits of 2gb on video data.
