I don't know what folder the offending file might be. It depends where it comes from.
You can use the free AFCAD utility, to help you finding duplicate AFCADs. First, you need to download it, it's a available at all the major site, it's made by Lee Swordy.
Once you have it installed, open an airport giving its ICAO code, KJFK in this case, and AFCAD will list all the files that are related to it. There are usually at least 2, one labeled "Stock", which is the default and you need to left untouched, and the one that comes with FSDT KFJK, which is located in the fsdreamteam\jfk\scenery folder.
If you have more than 2, take note of where they are located, then exit and remove them.