As I've said, nobody ever writes to the scenery.cfg files, except the installer so, if anything strange happens to the Scenery Library, it's nothing we do, but something that happens on your FSX install.
Note that, although you might not SEE any changes to the scenery.cfg, that file is not the only one that has an impact on the scenery library. There are also the scenery caches indexes, located at %ALLUSERSPROFILE%\Microsoft\FSX in the "SceneryCache" and the "SceneryIndex" folder, that control the scenery library, and are updated when you touch the scenery library menu.
We don't touch those files as well so, there's no reason why they would become corrupted, requiring a refresh to work again.
The next time it happens, as soon as you don't see the buildings anymore, DO NOT EXIT from FSX, and pay attention if you see the BOTH the Addon Manager and the "Couatl powered plugin menu" under the "Addons" menu, and report back.
And, as I've said, DO NOT try to fix the problem by refreshing the scenery library but, instead, exit from FSX, re-launch it again, and try again. If it doesn't work, DO NOT fix the problem by refreshing the scenery library but, instead, reboot Windows. Each time you do this, always check if you see BOTH the Addon Manager and "Couatl Powered pluings" menus under the "Addons" menu, and don't try just once and decide it doesn't work if you only tried once, but at least 2-3 times, and each time note if you see BOTH menus.
And no, I'm not saying you should do this normally, it's not normal at all, and it should't happen. But, you HAVE to do this for the time being, so we can understand WHY it's happening.