I'm having the exact same problem. Using the latest stable version (v2.0.1) on mac.
This is what I experience, when making changes to a floppy disk.. Per default, it makes an .sdf file in the "Save States" folder, containing disk changes. If I enable "writable_floppy_images = 1", it makes an .adf file in the "Save States" folder.
It never writes to the original .adf file, which is what I also want. Maybe it's a bug?