Trying a man for murder in the 1979 disappearance of 6-year-old Etan Patz has come with obstacles created by the passage of time: Many witnesses, including the lead detective, have died. Memories of those still alive have faded.

And the piles of investigative records from the case include untold missing documents — some of them in three boxes discovered in a police storage room in just the past few days, even as the trial is well underway.

"The historical file is incomplete," defense attorney Harvey Fishbein said after news of the boxes surfaced this week. "It shows the fact that no one knows what happened in 1979, and the investigation's been massive and the fact that there are so many questions about this case is a real problem."

Defense attorneys say that paper trail is another reason to doubt the case against 54-year-old Pedro Hernandez, who gave a stunning confession to investigators three years ago, saying he lured Etan to the basement of the convenience store where he worked, choked him and dumped his body a few blocks away. Hernandez's attorneys say the videotaped admissions were made up by man with a history of mental illness.

Etan vanished on his way to school on May 25, 1979; his disappearance helped galvanize the modern-day missing children's movement. Over the years, the case bounced around between detectives and units and from local police to federal agents and back. Most of the historical documents in the file are not specific to Hernandez, because no one was focused on him. But prosecutor argue it doesn't matter, because over the years in New Jersey, Hernandez told a prayer circle, his ex-wife and a neighbor that he'd harmed a child in New York.

There's been no physical evidence. During his confession, Hernandez told detectives that he tossed the boy's book bag up onto a freezer in the basement of the convenience store.

"If the freezer is still there, the book bag should be there," Hernandez told detectives. But the shop was closed and cleared out in the early 1980s, its contents tossed, and it's not clear whether police were present at the time. The owners have died, and the bag never made it into evidence. No body was ever found.

New York Police Department Detective Bill Butler was the case lead, amassing thousands of pages of notes and constantly walking the route Etan took to school. But Butler died in 1986 in an apparent suicide. His notes have been scattered and it's not clear from the official records how often or how extensive the searches of the store were.

Joseph Pollini, the former NYPD cold case squad commander now at John Jay College of Criminal Justice, said detectives' notes nowadays are highly detailed and computerized. But then, the practice was to keep the handwritten or typed records short.

"Probably the most important thing a detective can do is document their investigation so that anyone reading the paperwork could close their eyes and see what he saw," he said. "But that wasn't always the thinking."

In the early 1990s, federal authorities took over when it was thought Etan may have crossed state lines. Assistant U.S. Attorney Stuart GraBois built an extensive case against another suspect, Jose Ramos, a convicted child molester who remains in jail. Ramos was never charged but was found liable for the boy's death in 2001 in a civil judgment.

Manhattan Assistant District Attorney Joan Illuzzi-Orbon said late last year that some of those files were missing — a "disturbing" development. But for prosecutors, the challenges aren't insurmountable.

"When you think about the kind of evidence that the prosecutor would want to use, the parents talking about the last time they saw Etan, his movements that day, that information doesn't really change," said Bennett Capers, a former prosecutor and law professor at Brooklyn Law School.

The three boxes of evidence found in the police station that houses the missing-persons unit contain police records from the investigation, notes from an assistant district attorney who worked on the case and handwritten memos from a detective who investigated Ramos. Some of the information involves two informants who were working with prosecutors to try to link Ramos to Etan's death. Other boxes contain missing-person posters, records of people arrested and catalogs of files made by the original detective on the case. Defense attorneys said they needed time to go over the information and that it could result in re-calling some witnesses or even a mistrial request, though Fishbein said he wanted to finish trying the case.

Pollini said it's not an unusual development in such an old case.

"Papers get stuffed in desk drawers, they get thrown in the basement when a precinct is remodeled, they turn up in unusual spots," he said.

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