I think you guys get the law a lot better than you think you do! You are honing right in on what the significant issues and contradictions are.
The fact Casey filed a counterclaim in the civil suit doesn't waive or erase her 5th amendment rights. They take precedence. But if she takes the 5th, she can't have it both ways in the civil case, which the judge has allowed to continue. You can't pursue a claim, but refuse to give information in the claim against you. Her counterclaim may get tossed out of court, and she could even lose the main case eventually. But we aren't there yet.
As to the A's, if they are validly subpoenaed and the court doesn't excuse them for medical reasons, then they have to answer questions, even if they aren't relevant. That isn't the test during discovery in a civil case. They can each invoke their own 5th amendment rights, even though no criminal charges are pending now. They can't refuse to answer things because it might incriminate Casey. That is why they don't want these depositions, of course. If they just refuse and don't comply with valid court orders, then they can be sanctioned. Those can range from being forced to pay the other side's attorney's fees, contempt, etc.