Eu olho na manpage explica ...
-H, --hard-links
This tells rsync to look for hard-linked files in the source and link together the corresponding files on the destination. Without this option,
hard-linked files in the source are treated as though they were separate files.
... o que é aparentemente o que está acontecendo aqui ... então esquecendo as últimas horas e tentando rsync -Aav -H /mnt/old/backup/* /mnt/new/backup/