The three were among five adults arrested after 11 children were found living in filth on the compound and the body of a 3-year-old boy was retrieved. That body was later identified as missing Georgia boy Abdul-Ghani Wahhaj.
>> On WSBTV.com: Duo tied to New Mexico compound planned attack on Grady hospital, documents show
Prosecutors could still try to pursue charges by seeking an indictment from a grand jury. Prosecutors offered no immediate indications Wednesday as to how they will proceed.
Another hearing that happened later Wednesday dealt with new charges filed against the dead boy's father, Siraj Ibn Wahhaj, and his partner, Jany Leveille. They pleaded not guilty Wednesday to new charges of child abuse resulting in death after lesser charges were dismissed against them and other members of their extended family as the result of a deadline missed by prosecutors.
>> On WSBTV.com: 'I couldn't save him': Local mom devastated after remains found on New Mexico compound
The judge dismissed some of the charges against the two men.
Siraj Ibn Wahhaj is accused of taking his son, Abdul-Ghani, from his Clayton County, Georgia, home and bringing him to the compound.
The upgraded charges of child abuse resulting in death against Siraj Ibn Wahhaj and Leveille are tied to an extensive account of Abdul-Ghani's death in a journal that prosecutors attribute to Leveille.
The surviving children on the compound told investigators about religious rituals performed on Abdul-Ghani, saying the boy would cry with his eyes rolling back into his head as “jinn" and "shayateens," or spirits and demons, were cast out of him, sometimes for up to five hours a day.
>> Read more trending news
After the child's death, they said regular washing of his body would be used as a "tool of punishments against one of the children, if he disobeyed the requests of the adults or showed disrespect."
Prosecutors said in court filings they discovered a handwritten document called "Phases of a Terrorist Attack" that was seized from the compound and includes vague instructions for "the one-time terrorist" and mentioned an unnamed place called "the ideal attack site."
2 Men Arrested After Women, 11 Children Found Starving At New Mexico Compound