This question doesn't have much to do with JFK scenery, because it would more be a question for ADE (or whatever you use to edit AFCAD files), how to use it, how to install it properly, and how to be sure the version you have is correct.
I've just tried opening the AP_KJFK.BGL that comes with our JFK scenery with the current version of ADE, which is 1.37.5, added an airline code to a gate, than compiled it back to BGL, it worked just fine and created the BGL without any problems. And, to be sure even more, I've reopened the compiled .BGL with ADE again, and it showed up just fine.
So, I don't know what you are doing but, I can only confirm that, our original unmodified AFCAD, can be safely opened, edited and compiled again with the current version of ADE. Of course, if you are trying to open a replacement BGL with the same name, which came from somewere else, we can't obviously have any idea how that file was done.
If you are not fully sure how to edit a BGL yourself, then just don't do it, report to us what you would like to be changed, and we'll try to do it ourselves.