That is unfortunately the correct files (unfortunate as in: if it wasn't, fixing this would be easy)
Have you by accident changed the checkbox state next to the modification in the tree of the advanced userinterface.
The checkboxes have three states:
Cleared: Do not include this modification
Checked: Include this modification
3rd state: Include this modification if the folder it is in is included.
I recommend leaving the checkboxes at the 3rd state except the "Community Modifications" root node - that should be checked.
As it can be a bit difficult to see what will happen when the 3rd state there is another visual clue: If the modification is "grayed out" in the tree it will not be in your Flight Simulator, as the checkbox states of the modification or one of the parent folders deselects it.