change it to
App.ExecutableWin=1690800\Engine\Binaries\Win64\FactoryServer-Win64-Shipping.exe
App.ExecutableLinux=1690800/Engine/Binaries/Linux/FactoryServer-Linux-Shipping
make sure you shut down the instance before editing it (as in shut it completely down, not just the app but the whole instance) then when you start it up hit the start button and its going to verify the game files again and then will start the server up. also case is important so dont do any lower case where i have uppercase or it wont work.