ADE support is in FSDeveloper.com forum, there is a forum specifically for ADE in MSFS.
My troubleshooting usually ends up taking place in the airport xml code. Here you have direct control over AirportDelete options to retain or remove stock elements such as freqs, waypoints, ILS etc.
I’m slowly coming around to retaining all freqs, waypoints, procedures and ILS to be compatible with Navigraph addon. The trick here is to go to your C:…\AppData\Local\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe\LocalCache file content.xml and move Navigraph to the bottom of the list and this puts it in higher priority than all other addons.