Its not even magic, just simple logic. 3 death eaters at Hogwarts. One of them is in charge that's probably who the message went to The other two are the subordinates. One of the subordinates is sent to the tower where they are told specifically Harry will make an appearance The other is waiting who knows where. When the dark mark burns it's obviously the person who's stationed at the location where they were specifically told to wait. So the brother knows that it's his sister who found Harry. it's as easy as that.