how diff between hardlink trees works?

Hi, I am not able to understand how diff between two trees of which one is just contains hardlinks to another's files (cp -al )ing works.I am asking this question here because I need to build a custom kernel for which I need to generate patch. So the documentation suggests to create a hardlink copy of the kernel source tree using cp -al and then make changes to one of the trees and run a diff.I am wondering that if files are hardlinks then changes to one copy will affect another in which case diff should give no output. Also, the patch I created looks a little odd as it contains complete modified files instead of just the differences. Please help! Thanks Vaibhav Jain