I owned this scenario but did not have it in p3d, among other things, is in the Addon Manager folder of the GSX installer.
The updated installer added it because you had it installed into another sim, likely FSX. Since the whole point of the new installer was to have a single location for all sceneries, with no duplications regardless of many supported simulators you had, it has consolidated all your installed sceneries.
Add-ons installed using the native P3D method, can be disabled from the Options->Add-ons menu.