HiI

make sure that you have cleared all the fssc files out of addon scenery folder of fsi found it alot easier to just use afcad2 to update my runways, taxiways, and aprons using afcad2 and then use fssc to place any buildings or macrosthe other thing is when you alter an airport in afcad2...you will see a choice for your airport...a stock which is the original and mod..the modified one

I just tested with neighbour airport Bromma ESSB addon from Swedflight Pro deactivated, a very popular addon for Stockholm flyers.... Now ESKB is same height on RW and sourroundings, has autogen and I