The long-running prosecution of the whistleblower was back in the ACT Supreme Court on Friday as the Commonwealth attempts to rewrite evidence recorded two years ago, saying time had rendered some of it inaccurate.

Barrister Jeremy Kirk, acting for the Commonwealth, says it would be unethical to present two-year-old affidavits - which Collaery's lawyers have not seen - to the court given how much had changed on the international stage.

"Matters of international relations are inherently dynamic," Mr Kirk told the court.

The Commonwealth has kept evidence secret and pushed for closed court hearings saying the case had the potential to damage Australia's national security.

Collaery is accused of unlawfully sharing classified information about the alleged bugging operation of the East Timor prime minister by Australian officials in 2004.

Mr Kirk said it would make a mockery of national security laws to not include up-to-date evidence.

He said the Commonwealth was not seeking to introduce new evidence, which is what Collaery's lawyers are claiming, but rebalance evidence.

Justice David Mossop queried whether events on the public record like Australia's international spats and the former attorney-general's resignation would change the degree to which the evidence against Collaery prejudices national security.

The timing of the case has also drawn scepticism from Justice Mossop, who previously questioned whether the prosecution could ever end if the process to update the evidence takes in excess of a year given any appeals.

In a case fraught with technicalities and constant appeals, if the court took another year to rule on the evidence, as it did the first time, or it was appealed to the High Court, it could result in a perpetual cycle of updated evidence and challenges.

Collaery's lawyer, Chris Ward, argued the concern that the case would roll on in perpetuity was real.

He also argued it was unfair that the Attorney-General's Department was responsible for updating the evidence with what it considers relevant events in Australia's national security paradigm that Collaery could not respond to.

Dr Ward said such a process would lead to "irreparable prejudice".

Mr Kirk argued that access to evidence was an important discussion to have at a future time and said the updated evidence could go either way, potentially benefiting Collaery's defence.

"The defendant is happy to accept the benefit of the passage of time but is not prepared to accept the other side of the coin which is the evidence is updated," he told the court.

Collaery's legal team wants any outdated evidence removed and not updated.

Justice Mossop will deliver his ruling on whether he permits the Commonwealth to update its evidence on December 7.

Human Rights Law Centre senior lawyer Kieran Pender said the trial shouldn't be going ahead, especially in a closed court with secret evidence not even Collaery could see.

"There is no public interest in prosecuting whistleblowers," he said.

Australian Associated Press