Two papers rejected from conference. One of them was judged based on the other
I think you should mail the chair. It may be to no avail, but the chair will at least be informed of the practice.

Like you, I believe each paper should be judged on its own merits. Don't reject Paper B because you didn't like something in Paper A. That's truly ridiculous. But it could be a new rater who's unfamiliar with the process.