The airport will surely not "disappear" by themselves. But, if you are accustomed to selectively turn on/off areas in the Scenery Library, for example to turn off areas you don't need for a flight, you can't do that with our products, because the Scenery Library is read when FSX starts so, you need to restart FSX to make your changes effective.
If this is not the case, nobody has reported such problem so far in a way you are describing it, some users have permission/access problems, but that would only affect GSX, not the scenery itself.
Do you have another add-on that reads/writes the scenery.cfg ? Perhaps that one is getting access to the file, and has locked it preventing our software to access it at the same time. That would be the only explanation I can think of.
Also, be sure you don't run FSX in Compatibility mode. That will change all your file locations, so the scenery.cfg used will be a different one.
