I am having much the same issues with Airports not found in Navigraph and SimBrief.
My MSFS 2020 Version: 126.96.36.199
NNC Installs: NAVIGRAPH AIRAC Cycle 2203 Rev.1 ; Navagraph Charts In-Game Panel v1.3 ; Add on Package Aerosoft CRJ 550/700/900/1000
Example Plan successfully created and flown via MSFS 2020
Issue: in the Mid East, Saudi, Iraq, Iran etc, I am often unable to create/import a plan in Navigraph or SimBrief .
For Example in my current MSFS Plan OR0L-LTBA.PLN, the Airport OR0L exists in MSFS 2020 however it does not exist in Navagraph or Simbrief.
I did uninstall the non MSFS version of Navagraph (FDM?) and unloaded and reloaded the NCC packages mentioned above without success.