Our add-on.xml is 100% standard so, there's no special reason why you couldn't reactivate it from within the simulator interface.
You will surely have to restart the sim, because parts of the scenery are generated by the Couatl scripting engine software ( every interactive part, basically), which doesn't continuously re-check and rebuild its airport cache each time you use the Options-Add-on menu to re-enable a scenery, it only does that on the next sim restart.
I cannot explain why you don't see the scenery in Lorby, I can only confirm the add-on.xml is 100% following the most proper standard: it's located in the Documents\Prepar3d Addons folder ( 4 or 5 depending on the version ), so it's supposed to always work, at least it surely works when it's created by our installer, can't say what might happen if it's modified externally.
You said "it's not in my add-ons.cfg file", there are TWO add-ons.cfg files, one in %APPDATA% another one in %PROGRAMDATA%, both locations are valid, and by default, if you run our installer, you'll should find it in the add-on.cfg in %PROGRAMDATA%