You know, a few episodes earlier when the Chief Judge asked Bartlet whom he'd nominate as his successor I did wonder about Mendoza, and sadly concluded that like Mandy - who was a regular in s1 - he suddenly seemed to be retconned out of existence. So by the time The Supremes came along, I wasn't surprised he didn't show up. Still, you're right, it's a huge continuity problem.

And yes, the Whedonverse is tops in that department.