No, I did not have use_atomic_file_saving
on. However, I did have use_gio_unsafe_file_saving
on. The page you linked 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?
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