No... I forget the specific term but in court you can bring in multiple points of contradiction that are all contradictory to your other arguments, but would not be contradicting to your case, because they all contradict your legal adversaries case. The example as I heard it is A man is bitten by a neighbor's Pit Bull and the man takes takes his neighbor to court for damages. The neighbor mounts his defense by saying 1.) I don't own that dog. 2.) If I did own a dog, I wouldn't own that breed of dog. 3.) I always keep my dogs on a leash when I take them out of the house and would pull it away before it bit someone. 4.) On the day in question my dog was in the kennel.
In this case, the defense would be valid because the Plaintiff would have to disprove all 4 statements, any one of which would impact the case against the neighbor. In a criminal case, the defendant doesn't have to prove his story is true, he just has to prove that the Prosecution's story isn't. In a civil case, both sides merely have to prove their story is more likely to be true than the other side's. What's more, none of those statements is contradictory, they only seem so (Neighbor doesn't own that dog (he dog sits for his sister). If he did own a dog, it would be a different breed (He doesn't like Pitt Bulls). He never takes a dog out of his house without putting a leash on the dog and maintains control of the dog (Because that's what any dog owner would do). The dog was in the kennel on the day of the incident (because for his own reasons, he can't dog sit for his sister.)).
In effect, to avoid damage, the argument of "That's not my dog" is to argue that the neighbor isn't the responsible party for the dog's behavior. The second argument is that the neighbor would never own a pit bull even if he did own a dog, the third would demonstrate that even when there is a dog that the neighbor is caring for, he does so in a responsible way AND the dog being in the kennel shows that the dog couldn't possibly have been the one who bit the plaintiff.
What's more, the defendant can counter sue his neighbor for harassment, who just plain hates Pit Bulls and has been shouting at defendant for daring to care for his sister's dog even on days where the dog is not on the man's property and instantly blamed the Defendant in court without considering the possibility that there could be another Pit Bull owner in the area and their Pit Bull got loose.
In OP's case, the filing of a countersuit is just "Hope for the Best, prepare for the worst". They could be filing because the appellant court's decision may not come out in the window of time they have before they lose the ability to file counter claims. In that case, if the appeal goes in their favor, the suit is dismissed as well as the countersuit and goes to arbitration. If it goes against them, they will be arguing their claim at the trial.