Normally the FSDT Afcads are AP, now it seems that the newer Airports have a AFX afcad.
Do you mean the FSDT AFCADs ? You are being mislead by the filename: fact that some of them contains AFX in their name doesn't mean we use AFX to create them. And, we never used ADE to begin with, not even in the past. All our released AFCADs are compiled from an XML source code made by hand, and compiled with the official BGLCOMP.EXE from the FSX SDK started from a command line. AFX uses its own internal compiler.
There's no such thing as a "safe to edit" AFCAD, from the point of view of the AFCAD, our AFCADs are 100% standard with nothing out of specs inside. Your editing options and if it's safe or not to edit and save back it's ONLY dependent on the capabilities of the editor you use, and they might change from release to release.
One issue ADE used to create was the fact that we usually use the "DeleteAllApproaches" parameter set to False, so the AFCAD will just use the approaches from the default AFCAD, which of course make sense, since there isn't any need to duplicate all Approaches data, if we haven't changed any of them. I don't know how the *current* version of ADE handle this but, with previous version you couldn't control this and it saved back the AFCAD with the DeleteAllApproaches set to True, so you lose all the approaches, since the scenery didn't defined any. It's being a while since I've checked ADE so, it's possible this has been fixed in more recent versions. And even if it hasn't, it's always possible to generate an XML, change the parameter by hand, and compile manually with BGLCOMP.
In any case, it's not a problem of the AFCAD itself (the command is 100% standard and makes a lot of sense to use) but of the editor you use. AFX, in fact, never had this issue in the first place.
Note that, by editing AFCADs, there's the risk you'll disrupt GSX customization, especially if you renumber or rename parking spots, and surely if you rename the whole file.
And, whenever you launch either the GSX or the Stand-Alone Addon Manager installer, it will download all the AFCADs of all your FSDT installed sceneries and if you launch a specific scenery installer, will download its own AFCAD too, if it finds the existing one has been modified and it's not bit-per-bit identical to our online version. It WILL make a backup of your existing file so, you will never "lose" anything, but you will have to replace your modified file each time you run one of those installers and, you *might* miss some small fixes we might release to our AFCAD.