UAE by default does not write to ADF files, but makes an overlay file located in ~/Documents/FS-UAE/Save States
This is fine but it you want to alter an ADF to take back to a real Amiga this is useless as the overlays cannot be used.
However toy can tell UAE to write to the ADF by adding
writable_floppy_images = 1
Into the advanced settings.
If you need to “merge” an ADF with the changes stored in an existing overlay image, you can use writable_floppy_images in combination with a new ADF image and perform a disk copy from inside the Amiga.