I have also created missing airstrips in the SDK, only to have Asobo later on release one that stepped all over mine. I have been able to work around using Runway Delete and reloading Little Navmap Scenery Library.
But, here is a twist. Asobo created 2 Takotna airports in Alaska. PPCT and TCT are the same airport, but they created 2 separate ones that overlap each other. They both have asphalt runways by mistake. Is it possible to delete one of these reduntant airports so I can make modifications?