The Innocence Project at the Osgoode Hall law school in Toronto filed the charter challenge on behalf of Amina Chaudhary, who was found guilty in 1984 of killing her lover's eight-year-old nephew.
Chaudhary, who is currently out on day parole, continues to claim innocence despite losing an appeal and an application to the Supreme Court of Canada.
She has asked the federal government for a ministerial review of her case.
Her lawyers say key evidence that could help clear her name has disappeared due to what they call "arbitrary and inconsistent" preservation rules.
While the case originally centred on the missing autopsy photographs, lawyer Alan Young argued Wednesday the rest of Chaudhary's file — including samples of hair and soil — may also be at risk.
Any further loss could undermine her chances in the review, and without a direct order from the court, authorities have no incentive to safeguard items that could eventually prove crucial, he said.
"She wants to have her conviction reinvestigated. She doesn't need some ruling about whether her rights were violated in the past," he told the three-member panel.
"There has to be some assurance that what happened to the photographs won't happen again," he added.
But any talk of future losses seemed to rankle the judges, who suggested they couldn't issue a ruling based on a possible charter violation that hadn't yet taken place.
They stressed that an earlier decision had found no violation in connection with the photos' disappearance, and any other loss might be viewed in the same way.
"We don't decide charter cases in a vacuum," Justice John Laskin said in the hearing. "We've got to have some factual underpinning to decide this."
Lawyer Robert Charney, who represents the Ministry of the Attorney General, accused Young of trying to argue a "brand new case" by raising issues that had never surfaced in the matter before.
Nothing indicates any other evidence is threatened, he said, noting the photos likely vanished before the current rules on retention took effect.
As it is, autopsy photos in Toronto must be preserved forever.
The panel reserved its judgment Wednesday.
A Superior Court judge last year dismissed the Innocence Project's request to have the lifelong preservation of evidence declared a charter right, saying Chaudhary had not suffered from the loss.
In his ruling, Justice Michael Dambrot also said such a move would grant convicted criminals greater protection than those still before the courts.
In those cases, it isn't considered a charter violation so long as the Crown can prove the evidence wasn't lost or destroyed due to negligence.
The Innocence Project wants the Appeal Court to throw out the ruling and issue its own declaration requiring that evidence be safeguarded until the offender dies or gives permission to have it destroyed.
Authorities could also seek a court order permitting them to dispose of evidence.
Young said that while each region has its own policies on when evidence can be wiped out, those typically rely on arbitrary time periods rather than the key question: "Are these items needed?"
Given that some convicted offenders have taken up to 30 years to clear their names, "it has to be lifetime," he said.
Chaudhary's case began over autopsy photographs showing injuries to the young victim's head.
During her trial, the now-disgraced forensic child pathologist Charles Smith testified the photos showed the boy may have been knocked out, allowing Chaudhary to strangle him despite an injury that kept her from using her left hand.
Smith, once considered one of the foremost experts in his field, was later found to have wildly exaggerated his expertise. His testimony led to several wrongful convictions.
The photos were not made exhibits in the trial and the Crown has said they cannot be found, the Innocence Project said.
The coroner's office has twice reviewed the autopsy results without them.