Sorry for the slow answer, but what you did was correct.
The game tries to save things in as safe of a way as possible. So it writes to the bak files, deletes the old save, and then renames the bak to the normal save file name. This way if something crashes in the middle of saving there is always a valid save file (instead of a half written file).
Depths of Peril, Kivi's Underworld, Din's Curse, Drox Operative, Zombasite, Din's Legacy, & Drox Operative 2