Our scenery is installed into the Fsdreamteam\JFK\scenery folder under the main FSX folder. The file is named AP_KJFK.BGL, and is probably the only one you don't need to be worry about, because is sure it's correct.
Instead, you should have followed my advice of using the ADE program to search for JFK-related files, because it's not granted that an AFCAD file will always be named like AF2*-something so, if you just search for it using the regular search, you might miss a file which might be related to JFK, but not be named AF2*-something...
THAT'S why I told you to use a specific AFCAD file utility, and the free ADE is absolutely fine to use with FSX, and is able to find every file related to a specific airport, regardless how it has been named.
In any case, once you have found all the AFCADs for JFK, you need to delete (or rename to something other than *.BGL) them all, EXCEPT the default one from Microsoft, which will surely not cause prolems, and the one we supply in the fsdreamteam folder.
NOTE that, there are TWO AFCADs in our fsdreamteam folder: the other one is named appr_KFJK.bgl, and it contains only Approaches. We do it like this, so users are free to edit the main AFCAD file without worrying of having to use an utility that doesn't destroy the Approach data when saving back, like the original AFCAD program. You don't want to remove this file as well so, even if it's for JFK, and it might look like a duplicate, it's not, and you shouldn't delete it.