I just tested it.......it works exactly like I stated above. What EA has done is treated both games as single entities just like you do with NCAA Football and Madden football every year. I bet you can play as many AF2 seasons as you want and create a seperate export at the end of every year that you play and then at the end of every season of the AFL you can import the export file for that coming season during the off season.
I'm not sure if you played NCAA and MAdden with the Draft Classes, but this works the same way.