You can use a program called adf2disk to write them back onto a real amiga floppy. I think most will fit on the floppy if you compress them with lha or zip. You can use winace for files bigger than 720k and split them up and use unace on the amiga.
You can find both unace and adf2disk for free on aminet. You basicly do this on amiga side: adf2disk filename.adf and then insert a empty floppy.