Depending on OS, you might consider: rsync -aSH --delete --update /source/ /destination if both file-systems are Unix/Linux. -S Sparse files remain spars

Depending on OS, you might consider: rsync -aSH --delete --update /source/ /destination if both file-systems are Unix/Linux. -S Sparse files remain sparse. -H Hard links are preserved. Caveat: Big O(inodes). Note the trailing slash on /source/ unless you want to copy to /destination/source/. -W does not seem like a win for your local-to-local use case but may be the default: http://rsync.samba.org/ftp/rsync/rsync.html http://rsync.samba.org/ftp/rsync/rsync.html