Comment 2 for bug 1572182

This is likely not a bug but a configuration issue. Did you change the value of the "various" preference `use_atomic_file_saving`? It is off by default for this very reason: it doesn't maintain metadata and attributes.

See https://wiki.geany.org/config/all_you_never_wanted_to_know_about_file_saving and Edit→Preferences→Various→use_atomic_file_saving.