Just an update:
In my setup (Windows 7 x64) there appear to be two currently updated scenery.cfg files:
C:\ProgramData\Microsoft\FSX\ scenery.cfg and
C:\Users\All Users\Microsoft\FSX\ scenery.cfg
These actually appear to be different views of the same folder. If I have both folders open in Windows Explorer, and edit one of the scenery.cfg files, and save, the Date Modified instantly updates in both folders. Either Windows has a mechanism for synchronising the two folders, or the two "folders" are simply two views of the same data. It has been suggested that it is in some way "safer" to edit the version/view in C:\ProgramData\Microsoft\FSX\
This whole set of folders C:\ProgramData and C:\Users\All Users seem to be the same. Both change whichever view of the file you edit and save, so it is not just the FSX data which is treated this way
These are in addition to the copies of the original (and unchanged) scenery.cfg file in C:\Users\xxxx\AppData\Roaming\Microsoft\FSX and C:\Program Files (x86)\FSX
RogerC