Johna: Don't sweat this one. It happens ALL the time. When I was rerouted from BWI departure to IAD departure, I was "checked-in" at BWI and given a boarding pass. But I missed my IAD flight.

And think about how many times you are "checked in with boarding pass" on a connection that you miss. Airlines deal with this thousands of times a day.

As Aubie suggests, this would only be a problem if your friend had given his boarding pass to the agent at the gate door and the physical count on the plane did not match the computer's count of boarding passes collected...