No these files are all fine and should be left alone. I'm no expert but from within the sim open the GSX menu and click the last option "customise aircraft position" or some such, this opens the editor and in the top left corner it'll tell you the name and location of the afcad in use by GSX, it should point to your orbx dir, if it doesn't then there's your culprit. If it does then at the top right of the same window is a small icon you can click to match the airport elevation, see if that works.