When you rename a file manually, you must select the "Restart and rebuild airport cache" option from the Couatl menu.
Also, it's not a good idea to remove the default AFCAD. It's possible that freeware scenery was made only as an enhancement of the default file, so it *requires* it. And, if it's made as an enhancement, so it's not self-contained (for example, if it only added buildings), GSX cannot use it, since it can only use a single file at time.
So, for example, a 3rd party scenery that doesn't include runways, taxiways and parkings, but only adds (for example), some parkings or buildings the default one, cannot be used with GSX. The solution, for scenery developers and user knowing how to use ADE, is to first load the Stock data in a project, than add any modifications, and save it back into a new folder, so the new AFCAD would contain all the required data, meaning it's a self-contained airport.