But these "APPR" files are apparently special. I mean, they are identified as AFCAD, but in program AFCAD 2.21, nothing can be found, except those navaids, which as you said, don't even belong to the file. Anyway, I don't need to understand all your technology.
They are AFCAD. Or, if we really want to use the correct term, they are standard SDK Airport BGL, that contains only the Approach section and the waypoint section. It's not "our" technology, it's 100% standard MS SDK compliant BGL, just in a separate file, and Flight Sim supports this.
You are confusing what FS9/X can do with the BGL file format, with what the AFCAD utility allows you to do and how it presents the data. Since the AFCAD utility doesn't support Approaches display and/or editing, it's perfectly normal you don't see anything when opening that file with the AFCAD utility, because that section is entirely ignored.
Since the APPR_xxx.bgl file contains ONLY Approaches, the AFCAD utility will show it as if it was an empty file. However, since the AFCAD utility recognizes it IS related to Chicago, it will also show all the navaids in that area taken from the default scenery, so you might have the wrong impression that file contains just navaids.
Also, if you edit that file and save it back, you will also LOSE the Approaches, because the AFCAD utility do not save them back if you edit the file.
THAT'S why we have a separate file for Approaches. Since users like to tweak the *Airport* AFCAD, if we put the Approaches together with the Airport BGL ( the AF2*.BGL file ), they would lose the ability to edit it without losing the approaches, because the AFCAD utility (which is the most widely used), don't support them. The new ADE, for example, can be safely used to edit AFCAD with Approaches inside, but it's for FSX only.
My target is to have what I call a "generic" AFCAD and to be sure it will work correctly.
Just follow my initial advice: ignore the Approach file, and edit the main AFCAD file for the Airport, remove the dummy runways and, eventually, remove any take-off/landing restrictions on the runways, this will obtain a file which is as standard as possible.
But what shall I do with both "APPR_KJFK.bgl" ?
Just pretend they don't exist...unless you want also to renumber the runways.
To my view, these kind of tunings are like blocking a hole by digging a larger one. Between two troubles, I chose the one who is, for me, the most less bad.
I perfectly agree. In fact, since we develop under FSX, we do the FSX AFCADs in the regular way without those tricks. However, FS9 users seems to be generally more of the "tweaker" type and they asked for these kind of customizations, so we just let them have it: the AFCADs that comes with FS9 is the result of some help by forum users.