As explained, many times already, if you have a registration or activation problem, the buildings will NOT disappear! The scenery will run perfectly fine for 5-6 minutes in Trial mode.
So, if you don't see the buildings from the start, it doesn't have anything to do with registration or activation, it's something else, like the Addon Manager not running for some reasons.
But if you see the Addon Manager menu, it means everything works correctly, from our side. The only thing that might cause buildings to disappear, is that you have an old version of the sceneries but, in this case, you should have seen a warning about it when starting FS9. However, try to be sure you are using the current version of the sceneries.
Also, something that might cause this it's your G3D.DLL still from 9.0 but, in this case, you should have seen a warning from the installer, and the installation would have been aborted.
Another thing that might cause buildings to disappear, is if you have set the Autogen density at the minimum setting. The slider should be at least on the 2nd notch.
Of course, check your scenery areas are flagged as Active in the Scenery Library.
If it's nothing of these, and your sceneries worked fine before you restored your FS9.EXE, then we don't have any other explaination, except that something you did has corrupted your FS9 install in other ways. Or, something else is wrong on your system, maybe the same thing that prevented the >2GB patch to work, which is not normal as well.