The boy's father, Stan Patz, filed a motion this week citing what he said was "a wholly unexpected and surprising turn of events" in the death of a boy whose disappearance sparked an era of heightened awareness of crimes against children.
Etan's parents won the 2004 civil judgment in a wrongful death lawsuit against Jose Ramos, who is in prison under separate child molestation charges. Ramos never faced criminal charges in connection with Etan's death.
Bodega worker Pedro Hernandez confessed to Etan's killing in 2012 after being arrested as a result of a tip, authorities said at the time.
But attorneys for Hernandez have long maintained their client has an "IQ in the borderline-to-mild mental retardation range," making him susceptible to a false confession.
The criminal case against Hernandez ended in a mistrial in May, when a lone holdout prevented the jury from reaching a unanimous decision. Jury selection in a new trial is scheduled to begin March 7.
Hernandez's defense attorney, Harvey Fishbein, said the timing of the civil filing is suspicious.
In a letter to the judge in the upcoming trial, Fishbein said the civil filing by the Patz familty was "a blatant assault on Hernandez's ability to receive a fair and impartial trial."
Fishbein wrote, "The timing of this court filing, and this immediate attending publicity ... raises profound questions that must be addressed immediately."
The attorney for the family, Brian O'Dwyer, denied the civil court motion was meant to influence the criminal case.
O'Dwyer said Stan Patz "wanted to correct the record" because the new trial had brought the situation "to the forefront" of his mind.
"If Julia and I were aware of the information and evidence against Pedro Hernandez in 2001, when this action was initiated, and continuing through ... when the judgment was entered, we would not have initiated and continued this action against Jose A. Ramos in court to hold him responsible for Etan's abduction and death," Stan Patz wrote in the affidavit.
The Etan Patz case has gripped the nation for decades.
The boy went missing in 1979 after walking to a bus stop, and was the first missing child to be pictured on a milk carton.
Hernandez is charged with two counts of second-degree murder for allegedly intending to cause the boy's death and for a killing that occurred during a kidnapping.
But his lawyer has said Hernandez is mentally challenged, severely mentally ill and unable to tell whether he committed the crime.
Hernandez has been diagnosed with schizotypal personality disorder, one of a group of conditions informally thought of as "eccentric" personality disorders, according to Fishbein.
Police interrogated Hernandez for 7½ hours before he confessed.
Ramos' name has also hung over the case for years. He was a convicted child molester acquainted with a woman who Etan's parents said they hired to walk him and other children home from school during a school bus-driver's strike.
As part of the parents' civil suit against Ramos, Etan was officially declared dead by the court.
A judge found Ramos responsible for the boy's death and ordered him to pay the family $2 million, money the Patz family has not received.
Ramos served a 20-year prison sentence in Pennsylvania for molesting another boy and was set to be released in 2012. He was rearrested on charges of failing to register as a sex offender soon after leaving prison.