NEW YORK (CBSNewYork/AP) — The difficulties in trying a nearly 36-year-old murder case were becoming obvious Tuesday in the trial of the man accused of killing 6-year-old Etan Patz.

The lead detective is dead, the crime scene — a bodega — no longer exists, and three newly discovered boxes of old evidence have been consuming the attention of defense attorney Alice Fontier, WCBS 880’s Irene Cornell reported.

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Fontier, who represents Pedro Hernandez, told the court she has found 39 pages of notes taken by a detective who happened to grow up in the same building where Jose Ramos lived. Ramos is the convicted pedophile long suspected in Etan’s 1979 disappearance.

The detective interviewed many people who told of seeing a boy with Ramos who looked like Etan. Fontier said the private investigator for the defense has been trying with no luck to locate the long-ago residents.

She told told the judge, “This could put us at a serious disadvantage.”

Ramos dated a woman who sometimes walked Etan home from school. He would later be accused of sexually assaulting boys in Pennsylvania and serve more than 25 years on his convictions. Ramos told authorities about interacting with a boy he thought could be Etan on the day he disappeared, though Ramos said he hadn’t killed the boy. He has since denied having anything to do with Etan’s disappearance.

Prosecutor Joan Illuzzi-Orbon told the court her team had no role in withholding the newly discovered evidence.

Earlier Tuesday, Harvey Fishbein, another defense lawyer, ran into a brick wall while trying to get any answers from the case detective, David Rivera.

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Nearly every question Fishbein asked was met with an objection by the prosecutor and then sustained by the judge, Cornell reported.

Fishbein’s questions centered on evidence the jury has already heard that there were few children living in SoHo in 1979, that the school bus stop where Etan was headed when he disappeared was not marked and that if Hernandez were doing his job — making sandwiches in the back of the bodega every day at 8 a.m. — he would never have seen the boy at the bus stop.

Fishbein told the judge, “Your honor, you’re tying my hands.”

Etan disappeared while walking to his bus stop on May 25, 1979. Hernandez was a teenage stock clerk at a bodega a few blocks from where Etan was last seen.

Hernandez confessed to police in 2012 that he offered Etan a soda to entice him into the store’s basement. Then, Hernandez said, he choked the boy and dumped him, still alive, in a box with some curbside trash.

The child’s body was never found, but he was legally declared dead as the investigation spanned decades.

Defense attorneys maintain that Hernandez is bipolar and schizophrenic and that his confessions are false.

Etan’s disappearance ushered in a new protectiveness into American parenting. He became one of the first missing children featured on milk cartons. His parents advocated for legislation that created a nationwide law-enforcement framework to address such cases.

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