We don't seem able to remove the default ILSs or NDBs and replace them with custom ones when replacing an airport that comes with the simulator. Not sure when this occurred, not had this issue before and our current airport (WBGR) has been in development for several months, we've only just got around to final testing which includes fine tuning glideslope position etc.
We were trying to reposition our custom glideslope as it seemed way out of position in flight, but any movement didn't make any difference to the touchdown point. The glideslope was removed from the runway completely and tested again, we found there was still an active glideslope for the runway even though there was none specified. We removed the ILS completely from the runway element and testing again gave us a VOR DME with glideslope that shouldn't be there. Our workflow usually sets up the initial XML manually based on the SDK documentation.
We've subsequently set up a simple airport replacement for WBGR with delete commands set for everything, and a simple runway using only the scenery editor. With the only compiled project in the community folder and nothing else, the ILS and DME are still shown on the world map. The project xml screenshot is attached.
As a cross check we have done the same for EGNM Leeds Bradford, replacing an existing airport using the scenery editor and deleting everything using the delete options in the airport element. The results appear the same with the default airports ILS and NDB being displayed on the world map and not being removed as expected.
We're a little stuck between a rock and a hard place at the moment.