open shell:
type:
makedir :sys
copy sys: :sys/ ALL
convert sys:
format sys:
copy :sys/ sys: ALL
You should use copy CLONE ALL.
Also, copy doesn't handle links at all, so if you have those you need to remove them first and recreate them after copying the files back.
If you have softlinks and want to avoid the hazzle, you can use tar or GeekGadgets 'cp -a'.
