I would have expected checked bags since it would have been easier to track where they needed to go.

The other thing to add is that instead of waiting to send the bags out on the next PHX-LAX leg (two hours later... it was my originally scheduled flight), they sent them out on the delayed Ted PHX-SFO flight. So, not only did they remove them from the flight, they sent them to an airport that would have no idea of what was going on...