I know it sounds strange, but it happened twice and only happened every time I was uninstalling FSDT products. I decided to leave the airports alone and only installed GSX.
It's not strange, it's basically impossible, because you are the one and only ever reported this. The only possible explanation is: one of your configuration files, likely the add-on.cfg, has been corrupted by ANOTHER product, most likely a bugged product that has installers that wrongly try to write that file themselves, and destroyed it by changing the encoding, which is supposed to be Unicode, but many bugged installers write it back to ANSI.
Our installers DO NOT try to write ANY of the P3D config files directly. They all follow LM guidelines that these files should never be touched by installers, and they should only use the P3D command line utilities, that use the simulator *itself* to make any changes to these files, both when installing and when uninstalling. However, if these files were corrupted ( change of encoding is the typical mistake they do ) by another application, it's POSSIBLE that, when our Uninstaller, which as a proper P3D-compliant installer delegates the change of these to the sim own facilities, results in the sim itself not being able to change the file, since it encountered a wrong encoding caused by another non-compliant installer that changed it.
That's the only possible explanation of why you have been mislead into thinking "Uninstalling FSDT corrupted my sim". What corrupted your sim was a non-compliant installer or a bugged installer, but you had to use a proper installer like the FSDT one, to realize its effect.
And yes, before you say "if the file was already corrupted, why I didn't noticed ?" and the answer is the actual simulator is more resilient against those kind of file corruption, and accepts files in both encoding style ( that's why many developers don't even bother changing it, the sim continue to work ), but the command line facilities all proper installers ( like ours ) are not the same routines as the one used while the sim is running, and they might be more strict about the file syntax, likely because they assume "everybody" would use them, so they don't expect those files might be changed externally by non-compliant installers.
Sorry for the lengthy explanation, but it's important to squash rumors about "GSX corrupted the sim", before they grow and spread into urban legends.