> 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 
https://github.com/geany/geany/pull/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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