It might be that information is not saved in the .sit file type. The manual says:
It is essentially a “snapshot” that makes a note of the aircraft you are using, its position in the air or on the ground, its payload, the amount of fuel in its tanks, and so on. It also includes information on the environmental conditions of the flight, including cloud conditions, temperature, and time of day. Furthermore, any other aircraft you have loaded will also be noted.
I will ask the developers if nav data should be included in the file or not.