It would be best if you could verify that that enabling `files.use_atomic_file_saving` fixes your problem - then we'd be sure the problem is the file saving method and not something else. That would however require something like this: 1. Disable `files.use_atomic_file_saving` and keep restarting your computer with Geany open until Geany loses the configuration. 2. Enable `files.use_atomic_file_saving` and do at least 2x the number of restarts than in (1) at which point we might assume the problem is fixed by this settings.
I'm sorry for you in advance ;-)
The settings `use_gio_unsafe_file_saving` doesn't matter for configuration files, it's currently only used for open documents.