They are made by the same factory, using the same shell. I am really, really not sure, just seat of the pants, not certain, please don't quote me because I may be wrong, etc. but I think the Fly version has a different, more round shape to the EPS liner. Important to be really careful with statements like this because so frequently one person describes a helmet shape as oval, while another may say the same helmet is round.
The AFX definitely fits bigger, 100% sure of this. It also seems more oval. I hope to eventually compare them back to back with several testers.
CRSpeedy, were you a Medium in the AFX and a Large in the Fly? Your descrip sounds like this is the case, because that is the shell break.
Hope that helps.