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.