that file contains ONLY the IFR approaches, there are no visible objects, so it's correct you have two AFCADs: the "main" one and the one for the approaches, that hasn't been updated in years.
It's separate from the main AFCAD, so you can choose which procedure to use for the 13L approach (and there's a sub-folder with the alternate procedure), by switching the approaches AFCAD without affecting the main one.
The problem is surely caused by another scenery in conflict, and the most common cause of conflicts are AFCADs supplied with AI traffic packages, like MyTraffic, Traffic360, etc.
If the FSX Airport Scanner couldn't find them, try to look for their folders for files with names that refer to JFK, and remove them manually-