are you using ver 3.66 I dad the same problem with this ver but now im using 3.0 I don't have the same problem
All sdl are 3.0 it only meansnit is for wow 3.And all 1.3 have the model deletion problem. Just dont save 2 times if younhave it open. After a save always restart noggit. Inwill try to get this fixed the next days.
The place you are located in noggit dont change the save function in any way. So it was just luck that you dont loos models saving the second time.