I won't pretend to understand why your copying hard links but if you keep it simple... do you have the same issue? and rsync handles sparce files very well with its on the fly hash checking anyway so unless you've got very large sparce files I would drop it..
give this a try..
rsync -rP <Source> <Destination>
see if you have the same issue..
Also I found hash checking files in my storage drive while rsyncing didn't really benefit me, if it needed to be synced there would normally just be a size difference.. the chance you've edited a file and its the same size would be extremely unlikely... (--size-only)
If this is for your Minecraft server or system backup then hash checking would still be worth doing..
Or this might even have to do with some strange time issue where its copying to the new drive and its time format has changed... Apparently ext4 has 2 more digits of accuracy... but I'm speculating, you could give --ignore-times a try