<p>No, I did not have <code>use_atomic_file_saving</code> on. However, I did have <code>use_gio_unsafe_file_saving</code> on. <a href="https://wiki.geany.org/config/all_you_never_wanted_to_know_about_file_saving">The page you linked</a> says that is on by default. Turning off <code>use_gio_unsafe_file_saving</code> fixes the problem, as it should, because the page says this results in simple overwrite file saving.</p>
<p>According to that page, <code>use_gio_unsafe_file_saving</code> does attempt to retain "metadata" but apparently that doesn't work for Windows permissions.</p>
<p>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?</p>

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