More specifically, I had fixed AFCAD for LJLJ before upload. GSX shows the SAME AFCAD and Location but it has now classified the gates by their AFCAD index number instead of by the actual GATE number.
Sorry, but this is not possible, the update doesn't touch ANYTHING in AFCAD of non-FSDT sceneries. The only modification you made to AFCADs would eventually "lost" ONLY if you modified an FSDT scenery, because all our installers (not just GSX) always download the most current version of the AFCAD of an FSDT scenery.
And, of course, no modifications are really "lost", since the installer obviously made a backup of your AFCAD BEFORE the installation, check the scenery folder.
And, I'll repeat it again, this matters ONLY to FSDT sceneries. No other AFCAD of any other airport is ever touched by GSX.
In reading the initial announcement, I may perhaps not have everything installed so I will try again to install. What files should I have if all is correctly installed? Manual does not discuss this.
There's no need for the manual to discuss files, since this is being dealt with by the installer. If you were supposed to handle files manually, there wouldn't be any need for having an installer in the first place.