Você tentou ln.exe com a função "Cópia Inteligente" --copy
?
Smart Copy basically creates a copy of the directory structure from the source location to the destination, but it preserves the inner hardlink structure and inner junction/symbolic link relations of the source, and recreates this inner hardlink structure and inner junction/symbolic link relation at the destination location
Smart Copy is a must if e.g. the whole content of a hard disk, which has lots of hardlinks/junctions/symbolic links, should be copied to another hard disk.