When a court in case #1 makes a decision on an issue that is also present in case #2 (and especially when that decision is confirmed by the Supreme Court of Canada), that decision becomes binding in case #2.  It's the law.

The finding that Canadian government officials violated Khadr's Charter rights in a serious manner, was made in case #1 (repatriation to Canada).  It was also an issue in case #2 (damages), and in fact a very major issue - it decided liability.

That's how the two cases are related, Roscoc2000.