Are you using 3.4? The SDK says the new scenery installation procedures should work with 3.3, but unfortunately that's not the case. You need to run 3.4.
It's the opposite way around. The new installation method using the add-on.xml system, which is the suggested installation method from the P3D SDK, works ONLY with 3.4 and the current version of our installers use it only from 3.4 and above.
However, that's precisely what prevents the sceneries to be deselected, because now, the proper place to deselect an add-on, is from the "Options->Add-ons" menu.
And, as explained so many times here on the forum, if the reason for wanting to deselect the scenery is to save memory, it's totally useless deactivating FSDT or Flightbeam sceneries just to save VAS, it's a complete waste of time and effort, because the Addon Manager already does custom memory management for such sceneries, by removing all objects created at the airport, the moment you exit from its area, about 15.0 NM out.