GSX reads the GSX.CFG file from both the FSX\Simobjects\Airplanes folder AND the %APPDATA%\Virtuali\Airplanes folder. If a GSX.CFG is present in the FSX\Simobjects\Airplanes folder, it will be READ from there but, as soon as you start making changes to it, a copy will be made into %APPDATA%\Virtuali\Airplanes folder and so THIS file will then have the priority over the one on the FSX folder.
The reason for this is being compliant with the Windows Vista/7/8 UAC rules, that no program should ever try to write into its own folder (under the FSX main folder), which is usually located under the non-writable C:\Program Files folder, but GSX still reads a GSX.CFG file placed in the FSX\Simobjects\Airplanes folder, so an airplane developer can supply a GSX.CFG file with its airplane alongside the aircraft.cfg, so it's easy to distribute.
This means, all your CFG shuffling, should be made into the %APPDATA%\Virtuali\Airplanes folder rather than the FSX\Simobjects\Airplanes folder.