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If all autosave/backup versions of the save files are deleted through windows the game will autosave properly until attempting to overwrite a save with a .bak version, in which case it will fail. In the event of the game failing, it writes a new .tmp save.
The game will fail to overwrite the save files no matter if the folder is set to Read Only or not.
Creating a new save with a different name will create a new save, but after continuing on the autosaves will eventually start to fail once they've cycled around enough times.