Fly II default models

I thought I would post this again and see if anyone has a solution.Many of the default Fly II buildings are out of position when you Terrascene the same area that the default buildings are in. For instance after doing the SFO area in TS2 many of the buildings are now in the bay, the Bay Bridge is completely off from the roadway leading to and from it and Alcatraz is in the water. You can move them in the editor but saving does not create a scnery file and when you restart Fly II the objects are back in their default position. Any suggestions on how to reposition them and have the changes stick?