As a general rule, after installing an older (KSFO) scenery after a new one (KPHX) it would be best to install the Stand-Alone Addon Manager. Of course, reinstalling the full GSX is basically the same.
The problem with the SceneryIndexes\ folder didn't had anything to do with KSFO and its installation, it's more like an issue that sometimes happens with FSX not updating the Scenery Library entirely.
GSX relies on that folder to detect it's time to update its own cache, we could make it 100% foolproof, by updating the GSX cache every time, but then it would be annoying because you would have to wait for the GSX cache at every FSX start so, we used the simpler solution, to rely on the FSX own cache to know when it's time to update the GSX cache too.