I don't know if there's an available tool to do it, but "assuming these sources are aligned in time, remove this reference B from that recording A" would be qui

I don't know if there's an available tool to do it, but "assuming these sources are aligned in time, remove this reference B from that recording A" would be quite a nice undergrad problem. You'd do something like cross-correlate A with B, multiply B by the correlation coefficient and then subtract the result from A. In the frequency domain, because that makes things a little easier. The next question on the problem would be "Give at least three reasons why this doesn't perfectly remove the reference sound," of course.