Lynn has maintained he is not guilty of murder, claiming instead the two deaths were tragic accidents.

He has admitted moving their bodies to remote bushland before returning months later to burn their remains. 

The pilot told the jury Mrs Clay was shot in the head as he and Mr Hill struggled over his shotgun.

He then claimed Mr Hill came at him with a knife and was fatally stabbed in the chest during a second struggle.

Lynn admitted he carried out "despicable" actions after the deaths, telling the jury he panicked and destroyed evidence because he feared his career would be over.

But prosecutor Daniel Porceddu told the jury Lynn made up this story and he had "obliterated all evidence" to conceal the murders.

In his directions on Friday, Justice Michael Croucher told the jury Mr Porceddu had breached the legal rule of fairness several times in his closing arguments.

The judge pointed to 16 instances where Mr Porceddu made claims that had not been put to Lynn or ballistics expert, Leading Senior Constable Paul Griffiths, during cross-examination.

They included claims Lynn wrongly told officers he scattered the burnt remains in a tree stump instead of a tree root ball, and that Sen Const Griffiths' evidence was open to speculation. 

Justice Croucher told the jury Mr Porceddu should have questioned Lynn and the ballistics expert about these claims as a matter of fairness. 

Because he did not, the judge said the jury could more readily accept Lynn and Sen Const Griffiths' evidence, and reject the prosecution's arguments.

The jury of 14 was reduced by two on Friday afternoon, as only 12 jurors are required to decide on a verdict.

Justice Croucher thanked the two jurors for their service, discharged them and offered to exempt them from jury service for 10 years. 

The 12 jurors will only consider whether Lynn is guilty of the two charges of murder, after the alternative manslaughter charges were thrown out.

The jury will formally begin deliberations on Monday morning.