ln, by Hermann Schinagl, is a command line hardlink utility for Windows. It can do a tremendous number of things with files and hardlinks that Windows doesn't provide a way to do, all of which are explained on its page in more detail than I could provide here.
Among other things, the --backup --copy combination of options can move an entire tree of files that have been hardlinked together in various ways, without breaking the hardlinks back out into files. Copying them with Windows Explorer will create a new file for each link, requiring another run of Clonespy to link duplicates together again.
ln is freeware. Download here.