Can I use AeroScenery to create AFS2 scenery from files I used to download with FSET?
No, unfortunately not. I save an "aero" file of metadata with each tile AeroScenery downloads or creates. It needs those to process things.
An 80 x 80km area shouldn't take too long to re-download with AeroScenery if you have a reasonable internet connection, even at zoom level 18.