From the moment Pedro Hernandez was indicted for the murder of Etan Patz, both prosecutors and defense lawyers recognized they faced a formidable task: locating, deciphering and sharing a vast array of information and evidence collected over the decades since Patz, then a 6-year-old boy on his way to school, disappeared in 1979. There were police reports, FBI files, former suspects, witness statements. SoHo, the neighborhood where the boy vanished, had been remade. The lead investigator had died. Residents had moved.

It took close to two and a half years, but at last, earlier this year, both sides declared themselves ready for trial. And then came word, weeks into the trial, that the 36-month effort to recover evidence had been incomplete. Three boxes of Patz investigative material turned up in a Harlem storage room, including one box that both sides acknowledged might include detailed material relating to a convicted pedophile who had once been the top suspect in the case.

In recent days, then, prosecutors were working to get the new material copied and turned over to the defense. The defense was talking about the possibility of a mistrial.

The development was the latest improbable twist in a missing child case that once captivated the country. Patz had been on his way to school on a day in May 1979, by himself for the first time. He never turned up at school. A giant manhunt was undertaken. Parents across the country debated how to keep their children safe. People falsely claiming to be the boy turned up over the years; the body was never found. A decade ago, the boy’s parents had their son formally declared dead. They later won a civil wrongful death judgment against the longtime chief suspect: Jose Ramos, a pedophile who had once had a relationship with Patz’s babysitter, and who, according to one prosecutor, had all but confessed to killing the boy.

But Ramos is not the man currently on trial. In May 2012, a former bodega clerk from the Patzs’ SoHo neighborhood out of the blue confessed to strangling the boy in the bodega basement and stashing the body in a box he later placed on a nearby street. The city was shocked. The boy’s parents were cautious. Lawyers for the former clerk, Pedro Hernandez, said the confession was a mentally ill man’s fantasy and the fruit of manipulative work by detectives eager to solve one of New York’s enduring mysteries.

When Hernandez’s trial began this January, defense lawyer Harvey Fishbein made clear he intended to argue that Ramos was the more likely killer. And he was going to rely on the reams of material that had been generated over the years that some investigators had once hoped would be used against Ramos: his own statements; his alleged access to the family through the babysitter; the accounts of two informants who had shared a prison cell with Ramos over the years and allegedly drawn him out on the Patz case.

Now, with the discovery in Harlem, Fishbein may have access to additional material to aid in his defense. On Monday, when news of the discovery became public, Fishbein said it was unclear whether he’d move for a mistrial, but he and his team suggested there could be important information in the boxes. They indicated that witnesses who have already testified may have to be recalled, and that new possible witnesses might be required to appear.

“At a minimum, it shows the historical file is incomplete,” Fishbein told reporters on Monday.

Prosecutors are obligated to turn over any material in their possession that might have a material impact on the case, even information that may be beneficial to the defense. If they fail to, intentionally or as the result of an honest mistake, a judge may rule that the chance at a fully fair trial has been lost.

Bennett Gershman, a professor at Pace Law School, said it was unusual but not unprecedented for such discoveries to happen during trial. He said the trial judge, Maxwell Wiley, bears responsibility for sorting out the significance of the new material. He may decide that both sides can work through the material and the trial can proceed. On Tuesday, both sides were back in court, going forward.

But the judge could decide a mistrial might be warranted – even if the defense objects. He could determine that any need to re-question witnesses and the like would prove too confusing, even overwhelming for the jury. Such actions are rare and could invite the question of whether Hernandez could be re-tried at all.

“No one is really faulting anyone,” Gershman said. “It could be much ado about nothing. The key issue is carefully going through all the material.” Prosecutors said the boxes were discovered by the New York Police Department while cleaning out a storage space on Frederick Douglass Boulevard. Among their contents:

A police interview of Ramos; index cards for everyone interviewed in the case; a card for every psychic used in the case; alleged sightings of Patz; letters to the Patz family that they gave police over the years, including reports of sightings and notes of condolence; the debriefings of an informant in the case, and case notes from a detective who interviewed residents of Ramos’s 1979 Manhattan residence.

Prosecutors with the Manhattan District Attorney’s office in court on Tuesday said the lost boxes represented no bad faith effort to conceal anything.

A defense lawyer, Alice Fontier, said the material amounted to thousands of pages that they had yet to fully examine. She also said that the notes found of the detective – he had lived in Ramos’s building as a child and years later interviewed tenants who had once been his neighbors – indicated numerous people had recalled seeing Patz in the building with Ramos and his girlfriend.