First, having the two AFCAD in this way is perfectly normal and allowed by Flight sim. The appr_KJFK.bgl contains only approaches, and the AF2_KJFK.bgl contains all parkings, this is absolutely 100% correct.
The problem it's just FS Navigator that, apparently, only enables one AFCAD per folder, but Flight sim can handle this normally.
The reason for having splitted the airport from the approaches, was to allow users to edit the main AFCAD freely with any tool including the old AFCAD program without worrying about losing approaches because, when JFK was released, there weren't tools that allowed to edit an AFCAD and save it back without losing the approaches.
And, because you can switch between the two provided approach sets for 13L, one with the ILS and the other with the visual Canarsie procedure.
So, the problem is really FS Navigator, that should be improved to allow that is absolutely normal and possible in Flight sim, two layered AFCAD for the same airport that are doing different things.
About your problem of texture resolution, that's not obviously a problem of the scenery, but your video settings: your overall image quality is very bad, because you are not using the Anisotropic filter in your video settings.
To get the best image quality, use these settings:
- MipMap size in FS9 at 5
- Global Max texture size in FS9 at the highest setting.
- Anisotropic filter setting in your video card control panel set to override the application setting, at 8x or 16x.
