I'm not sure I'm following you there. Like I said in https://github.com/geany/geany/issues/3946#issuecomment-2345794726 the option is already unchecked. I don't really understand what you want me to do exactly...
In (1) above to verify you are still able to reproduce the issue (by having `files.use_atomic_file_saving` unchecked).
In (2) to verify that checking `files.use_atomic_file_saving` fixes the problem.