Tuesday's felony settlement conference in Riverside was the first step as prosecutors and defense attorneys explore resolving the case through a possible plea agreement.
In the meantime, their infant son remains missing.
Emmanuel was reported missing on Aug. 14. His parents were arrested in the baby's death and pleaded not guilty on Sept. 4.
Baby Emmanuel's dad denies claims that boy was victim of long-term abuse in new jailhouse interview
"The filing in this case reflects our belief that baby Emmanuel was abused... over time, and that eventually, because of that abuse, he succumbed to those injuries. That's what we believe," Riverside County District Attorney Mike Hestrin said at the time.
The child's parents were taken into custody last month following a multi-agency investigation into the disappearance and presumed death of their baby son.
It began Aug. 14, when Rebecca said she was attacked and the baby kidnapped in a Big 5 parking lot in Yucaipa.
Questions were raised after authorities said there were inconsistencies in the parents' story, leading them to search their Cabazon home multiple times before they were arrested and charged.