They will resume discussions tomorrow morning in search of unanimous verdicts on the two charges of murder.
Justice Simon France, during his summing up, said he may address them on the possibility of a majority verdict later.
Lundy will remain on bail while the jury considers its decision.
Lundy is accused of hacking to death his wife Christine and their 7-year-old daughter Amber in their Palmerston North home in the early hours of August 30, 2000 and the court has heard evidence over the past seven weeks.
Justice France acknowledged the first trial in 2002, at which Lundy was found guilty, but told the jury to shelve any views they had about that.
"It's important you reach your verdicts on the basis of the evidence you've heard," he said.
"Put aside anything you thought you knew about the case before it started, anything you heard or read outside these four walls."
Justice France also discussed evidence the court had heard about Lundy using an escort hours before the alleged murder.
"Whether you approve of that from a moral viewpoint doesn't matter to your task. If you think it relates to their relationship it might have relevance, but don't judge him because you don't approve of a married man using a prostitute."+
When the jury retires to consider their decision - likely to be this afternoon - the judge told them they would be required to reach unanimous verdicts on which the seven men and five women agreed.
It would only be "much later on" that he would consider a majority verdict of 11 to 1.
Justice France said the scientific evidence from "recognised leaders in their fields" might be difficult to assess because the intellectuals disagreed on many points.
"But you have an advantage over those experts because you know all the evidence. You have the broader picture," he said.
"None of that means you should ignore the evidence of the experts; just don't get overwhelmed by it."
Justice France has spent the morning summarising the key points relied on by the Crown in attempting to prove Lundy was the killer and the defence in its bid to clear him.
Lundy's lawyer David Hislop, QC, sought to show that the central nervous system tissue found on the defendant's polo shirt could have got there through contamination.
But Crown prosecutor Philip Morgan, QC, highlighted the forensic evidence as clear proof he was the killer.
The polo shirt was found by police, inside out inside a suit bag in Lundy's car and the Crown submitted there was no way the tissue could have been accidentally transferred.
Another gaping difference between the two sides was in their opinions on the way the case was investigated.
Mr Hislop told the jury in his closing police computer expert Maarten Kleintjes and Dr James Pang - who gave evidence on stomach contents and time of death - changed their stories from the first trial.
Justice France was also critical of the pair but said it was up to the jury to decide whether their evidence amounted to the police showing "tunnel vision" in its original investigation of Lundy.
The judge described the scientific element of the case as "very significant" and distributed a factsheet to the jury.
The defence had sought to discredit the evidence the Crown relied on about the tissue samples on the polo shirt but Justice France said the jury should not reject it just because it was cutting edge.
"The fact that it is new does not mean you can't rely on it," he said.
From the start of the trial the Crown submitted the murder weapon was a tomahawk or small axe, despite it never being found by police.
"The evidence shifted back and forward quite a bit," Justice France said.
Some neighbours said Lundy did not have a tomahawk and borrowed theirs but in December he produced one for investigators.
"What you make of that is a matter for you," the judge said.
The financial pressures on the Lundys was put forward by the Crown as a motive - that maybe the defendant cracked because of their problems and he had also recently increased their life insurance policies.
"Small businesses owing money to people and being owed money by others isn't at all unusual," the judge told the jury.
"The vineyard venture probably wasn't so flash."
- NZME.
- NZME.
