The default setting is `use_gio_unsafe_file_saving` which does the same as `use_atomic_file_saving` __and__ fixes the protections __and__ handles MS file systems that can't rename in some circumstances, such as files on cheap file servers. So its best to leave it as is.
But as @techee says those settings don't affect writing config files, session files and project files, so it would be a good idea to change it to something safer, either `g_file_replace()` since `g_file_set_contents()` but that might have issues on Windows. In fact that may be why Geany does not use `g_key_file_save_file` since it uses `g_file_set_contents`.
Oh wait, silly me, do it the Geany way, add an option for the file saving method for config files :stuck_out_tongue_winking_eye:
But as I said above, best to store everything along the way including modified buffers and settings and store nothing at shutdown.