Are those AFCAD files incompatible with each other, when GSX is concerned ?
Incompatible usually means they have different parking spots, renamed or moved parking spots, or parking spots that exists in a file but not in the other. Or different taxi/vehicle path layouts, or different runways.
If this is the case, perhaps naming the .BGL with the same name is not a very good choice, because GSX assumes that, if an AFCAD is really different, it should have a different name, which is usually the case with the vast majority of sceneries out there. For example, a common practice is to offer different AFCADs, one for AI usage, and one with Static planes and, since the main difference lies in the parking spots, the "static" AFCAD always has a different name, and this works perfectly with GSX, which associates an .INI file with its own AFCAD.
So, in your case, it might be enough to rename one of the AFCAD files, and perhaps make a copy of the GSX.INI with a different name, and edit the AFCAD name in the [General] section of it, to match the renamed file so, from now one, the files will be independent. Or, you can just rename one of them, and start a new GSX profile from scratch, your choice.
It might be worth suggesting to Imaginesim to use different names for their AFCAD, if they are really that different.
If, instead, the differences are minor, and don't affect parkings, taxi layout or runways but only, for example, different Exclusion zones for default objects ( this is the main thing developers have to fix when adapting a scenery to P3D V5: having to deal with a different default scenery ), it's not really a problem using the same profile with GSX and, in fact, it's best this way, so you won't have to do twice the work, just because you are using two simulators at the same time.
