I think that's the legal issue or question. The Senate being in session was a sham. There were two senators present, one to have the presiding chair, and the other to start and adjourn. Typical "sessions" lasted less than half a minute, and no business could have been conducted, as the body didn't come remotely close to having a quorum present.
I think the court will find this to be a political question, outside of its ability to decide. But, assuming arguendo it says the appointment was improper, I doubt the court also tosses the rulings. The court would more likely apply the "de facto officer" principle to past actions.