When using rsync to copy rsnapshot archives you should use the --hard-links option:

       -H, --hard-links
              This tells rsync to look for hard-linked files in the source and
              link together the corresponding files on the destination.  With-
              out  this option, hard-linked files in the source are treated as
              though they were separate files.

Thanks to this post: https://www.cyberciti.biz/faq/linux-unix-apple-osx-bsd-rsync-copy-hard-links/