Jackson walked out of Harris County Jail around 1 a.m. Wednesday. His whereabouts after his release are not known.
Jackson, who was homeless, was arrested more than a year ago as a suspect in the stabbing death of Flores.
Police say Flores was attacked as he walked home from his middle school in May 2016. A month later, Jackson was charged with the boy's murder.
The Harris County District Attorney's office announced Tuesday DNA test results trying to connect Jackson to Flores' murder were inconclusive.
Despite the results, the boy's family still believes Jackson is the killer. Guadalupe Flores, Josue's sister, says she has not lost faith in the system.
"Be patient. Be calm. Whatever happens will happen, no matter if we throw tantrums. It's just going to hurt others," Guadalupe Flores said. "The best thing we can do is just look out for each other, because that's all there is right now."
Houston police say they still consider Jackson a suspect, and the case is still an open murder investigation.
VIDEO: HPD chief Art Acevedo talks about Flores investigation
Houston Police Chief Art Acevedo called Jackson "the appropriate suspect and the most likely suspect" in the case, but said that prosecutors opted to further investigate the murder to prevent a situation in which Jackson is found not guilty and could not be re-tried should further evidence or witnesses surface after the verdict is handed down.
"People talk. Criminals have loose lips. There are people out there...who have information on this case, who can help us solidify this case," Acevedo said. "I urge folks who may have information to dig deep into your heart."
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