I know you asked Knight but since it's a problem which i countered to i can help you.
in the Module file Which is
in the line which addresses Memory to load
ScenarioPackFolder = Ewiger_Krieg\Scenarios
You should change the Ewiger_Krieg to it's Previous folder :WW2:
Therefor all the Modifications will be enabled but the EK reads the original map folder.
This line is at the first paragraph of the .Module File.