No, I did not have `use_atomic_file_saving` on. However, I did have `use_gio_unsafe_file_saving` on. [The page you linked](https://wiki.geany.org/config/all_you_never_wanted_to_know_about_file_saving) says that is on by default. Turning off `use_gio_unsafe_file_saving` fixes the problem, as it should, because the page says this results in simple overwrite file saving.
According to that page, `use_gio_unsafe_file_saving` does attempt to retain "metadata" but apparently that doesn't work for Windows permissions.
I'm okay with my current configuration now. I don't like that the default configuration fails to preserve permissions, but feel free to close this issue if you don't think it is a bug. Maybe it should be considered a gio library bug instead?