I am in the minority, but I think he could have won an appeal for the first murder conviction. Much of that case was based on the other case- the one he was acquitted of.
That's not how appeals work. The higher court is looking to see if the procedural and legal decisions in the trial were correct. They do not look at the specific evidence used to obtain the conviction unless it shouldn't have been allowed in. And even then, if the record is clear that a jury could still have reached a guilty verdict, it's often found to be harmless error.
Also, just because Jose Baez is a self-proclaimed best trial lawyer ever in the history of the world does not mean he could effectively argue that appeal. Trial attorneys and appellate attorneys are often very different. Trial lawyers argue to juries. Appellate attorneys argue to panels of judges. You can't charm an appellate court into ruling for your side.