Having a scenery not load is a new one for me, but I have seen partial scenery loads.
The fix was to move the missing scenery up to the top of the content.xml file.
I have the MS Store version of MSFS, my content.xml file is in:
c:\Users\<your-user-name>\AppData\Local\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe\LocalCache