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Is this a consequence of use_atomic_file_saving ?
Yes. If you want symlinks preserved, you need to use use_gio_unsafe_file_saving and have use_atomic_file_saving disabled. This is why this is the default settings.
If you compiled Geany by yourself, the fix from #3950 resolves the issue you had with config files and then you can set the save method to whatever you wish.
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