Am having the same issue when i try to edit the PMDG 747, i want to remove the aft cabin door on the 400F variant, and it "saves" it.
But when i reboot the sim the aft door still exists.
See the clip attached, from what i've experienced before. When you clicked on save the edit box would close and it would save the stuff you changed/edited.
Now what happens is that it does not close, it "saves" the changes. But when you restart the sim, the stuff you saved has not been properly saved and you have to redo the changes..