The girls — allegedly starved and neglected since birth — were taken from their south-side home last May, weighing 5.9 kilograms and 7.3 kilograms.
One of the girls, who can only be identified as "M," died in September 2012 after a judge ordered she be taken off life support.
The parents, who remain in jail, are facing one count each of aggravated assault and criminal negligence causing bodily harm; and two counts each of failing to provide the necessities of life.
Each will now face an additional charge of second-degree murder and criminal negligence causing death.
The couple, who can't be named, will be back in court Friday.
A preliminary hearing is scheduled for June.