It's clear that all problems were caused by Ezdok, which seems to be very unstable.
Your mistake was to assume that this was something related to our products, and started uninstalling and/or (which worse) probably removing things by hand, which would explain why you got messages about orphaned areas, which you shouldn't have, had you used only our uninstaller without removing any files manually.
The scenery.cfg is not used anymore starting with P3D 3.4 and up, so it's entirely normal you wouldn't see the sceneries there, since they are now activated by their add-on.xml in the Documents\Prepar3d v3 addons folder. If you used our uninstallers, these files would have been removed during the uninstall process, of course.
Reinstalling the sim wouldn't help, but you should first be sure to Uninstall all FSDT product using the Uninstaller in the Windows Control panel, and you must do it, even if you already removed the scenery manually, because the uninstall does extra clean up you might not aware of.
Uninstall all the FSDT sceneries, uninstall the Addon Manager and then SODE, then reinstall ONE product, GSX for example, check if it works, and report back. Don't touch anything.