@nivrig This is likely caused by disk image caching. The old, cached image is used unless if you rename the file, or if you replace the original file the changed file + cache will result in corruption.
In short: FS-UAE doesn't write to the original ADF file, but maintains "overlay" where the changes are written to. Thus any changes you've made will be lost if you just assume they're written to the adf and copy the file.
Where things to terribly wrong is when you replace the original ADF with a different one: Then the overlay applied on top of it will result in corrupt data.
This is totally insane and highly confusing (at least to me). It always gets people until they learn about it:
https://fs-uae.net/docs/floppy-disk-images/
Adding "writable_floppy_images = 1" to the configuration file will make FS-UAE write back to the adf, as one would expect.