Having duplicate AFCADs is always a problem and according to FSX Scanner, they have identical AFCAD features such Runways, Navaids, etc..
Al, the same thing happened to me and your right, you shouldn't have duplicate ADE's.
So, all you need to do is either remove or rename the older afcads named AP_KFLL.bgl and AP_LSGG.bgl to .bak or .off, either way will work, or just remove them. Now, if you have customized either of the ADE's your renaming/removing, then you'll have to either make those changes to the newer ADE's called AFX, or just use the newer ones. Keep in mind that GSX is looking for the ADE's with the new names, so if you work on the new ones, make sure to keep the names the same.
Like you, I had dups in both KFLL and LSGG as well, but renaming them fixed it for me, but I had some custom excludes in the older KFLL ADE I was using to get rid of the ships and cranes and will have to put those into the newer ADE that is now included.
For whatever reason, FSDT had gone from naming the ADE's as AP_XXXX to AFX_XXXX when they customized the airports for GSX and hence the reason you have dups and the installer didn't rename them like it did for all the other airports.