What GTK and Glib versions are you using? (see Geany `menu->help->debug messages` near the top).
You can turn gio file operations off in `edit->preferences->various->use_gio_unsafe_file_saving` which despite the name also turns off GIO reading.
Geany then uses the Glib `g_file_get_contents()` and `g_file_set_contents()` which don't use GIO unless its changed.
You can also turn off the `g_file_set_contents()` (which does a rename and other stuff, see my post above) and just use C output by `edit->preferences->various->use_atomic_file_saving`.