But rsnapshot created that large number of hardlinks incrementally. Without trying it there's no indication that rsync handles that better, especially as rsync

But rsnapshot created that large number of hardlinks incrementally. Without trying it there's no indication that rsync handles that better, especially as rsync with default settings doesn't preserve hardlinks as rsync builds a quite expensive data structure for them. I'm surprised that cp even worked. I wouldn't have had the balls to just use cp as it could just have failed. My strategy would probably have been to cp or rsync over the latest backup (so that new incremental backups could be immediately be created again) and then incrementally rsync'ing the previous backups with hardlink detection.