The Live Update should have updated JFK2 too but, when it has offered you the option to update the AFCAD, have you replied YES ? If you don't update the AFCAD, you'll have double jetways at JFK.
If you want to keep your old AFCAD at all costs, you must create an exclude file for JFK, this way:
- If you already customized JFK2 on your own, remove any .INI files related to JFK under %APPDATA%\Virtuali\GSX
- Start the simulator and enter the scenery customization page at JFK.
- Go to any parking and select/deselect the "Exclude radius" checkmark. It should be already selected so, you must deselect and select it again. It will trigger the creation of an exclude XML the Control Panel can compile into an Exclude .BGL
- Quit the simulator and start the GSX Level 2 Control Panel. You should have an XML source file ready to be compiled. Press the Compile button, and it should create the .BGL
- Restart the simulator and you shouldn't see double jetways anymore.
But I suggest to just update the JFK AFCAD, so you won't have to do all of this.