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.
The vacancy clause of Article II is the exception, not the rule. It is not designed to be an end run around the duty of the Senate to vet the President's nominees.
The Senate being in session was a sham.
Also, Presidents do not have the power to declare when a house in another branch is in recess as Obam did, or to adjourn Congress for a day to place his cronies in power. These would be clear violations of the separation of powers.
But, he will almost certainly have four votes in Scotus, so as usual, the outcome will be a cr@pshoot.