First, be sure you remove the Microsoft version using the Content Manager. If that doesn't fix it, try to remove your CONTENT.XML file, so the sim will regenerate a new one on the next restart.
The file is located here:
%LOCALAPPDATA%\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe\LocalCache ( MS Store version )
%APPDATA%\Microsoft Flight Simulator ( Steam version )