See my other two answers. Your uncle would most certainly have to be there. If there is a resolution proposed (by either side) your uncle has to agree to it in order for it to take effect. His attorney cannot plead guilty on his behalf, most especially in a murder trial.
In Sacramento, the trial confirmation is known as the trial readiness conference or trial settlement conference. If a trial date is just being confirmed, the in custody defendant does not make an appearance in court because his or her presence is not required. If the trial is going to be continued, then the in custody defendant has to be present to agree to the continuance or what we call "entering a time waiver". Don't know how they handle things in Clovis though.
Every county does it differently. In most counties, your uncle would be there although they would likely only bring him into the courtroom for a very short period of time. You should call his attorney.