I don't have FSGenesis and after using FSX Airport scanner I am getting these two files listed as duplicates:
KJFK_FSDT.BGL ---> File path: ...\FSDreamTeam\KJFK\scenery
appr_KJFK.BGL ---> File Path: ...\FSDreamTeam\KJFK\scenery
These are not obviously duplicate (we would't create a duplicate in our own folder!!), it's just that the approaches file is separated from the rest of the AFCAD, so you can choose to enable the canarsie approach or not.
I have deleted the old JFK from scenery library and moved those folders to a seperate location.
I can only confirm that missing jetways can only be excluded by another AFCAD in conflict. Not all of them might be found by that scanner, check if you have something coming from an AI traffic package.
Of course, this assumes you keep JFK V2 on top of the Scenery Library, which is where the installer puts it by default.
Also, if you use AES, you can't use it until is updated to support JFK V2.