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Anglican Primate Fred Hiltz (L), Catholic Archbishop Gerard Pettipas, Prime Minister Stephen Harper, Inuit National President Terry Audla, Assembly of First Nations National Chief Perry Bellegarde, Justice Murray Sinclair, and Governor General David Johnston attend the Truth and Reconciliation Commission of Canada's closing ceremony at Rideau Hall in Ottawa June 3, 2015.Blair Gable/Reuters

The most horrific stories of abuse at residential schools may never become public as the Truth and Reconciliation Commission prepares for a legal battle this fall to block the destruction of key documents.

Even though the commission wrapped up four days of closing ceremonies this week and has released its final recommendations, it is still fighting in court to preserve sensitive transcripts of stories told by almost 38,000 former students.

Not all former students support the TRC's position, and the legal case has created unusual alliances. Like the TRC, the Canadian government is seeking to preserve the documents, while Catholic churches and the Assembly of First Nations have expressed concerns about their potential release.

At issue are the personal stories of former students who suffered sexual or severe physical abuse – recounted during private hearings called an Independent Assessment Process (IAP). The adjudicated hearings were set up through the same out-of-court residential schools settlement that created the commission. Former students were eligible for financial compensation based on the severity of the abuse they suffered.

Former students had to consent to have their IAP testimony transferred to the commission so they would not have to retell painful stories.

However, well into the process, the commission discovered that IAP adjudicators repeatedly failed to inform former students of their right to transfer their stories to the TRC. Instead, the adjudicators had all parties, including the former students, sign undertakings of strict confidentiality.

The commission continues to fight this issue in court, and a hearing is scheduled for Oct. 27-28 in Toronto.

"The loss of these documents would be a blow to Canada's national memory of a significant historic injustice," the commission stated in its summary report, which was released this week.

Ry Moran, director of the National Research Centre for Truth and Reconciliation, said that, without the documents, key questions like which schools and which regions had the worst history of abuse will never be answered.

"Those are fairly fundamental questions," he said, adding that the answers could influence where governments should focus their support spending.

The research centre, located at the University of Manitoba, will house the permanent records gathered by the TRC.

Justice Murray Sinclair, the chair of the commission, declined to comment further on the issue Thursday because it is before the courts.

While the commission heard and recorded testimony from 6,750 former students, the IAP hearings heard almost 38,000 stories of sexual and serious physical abuse. Original estimates said only 12,500 former students would come forward.

Justice Paul Perell of the Ontario Superior Court ruled on Aug. 6, 2014, that the destruction of IAP documents should be delayed for 15 years, during which time the former students would be given the opportunity to consent to transferring their stories to the TRC.

The concern of the TRC is that obtaining that consent will be a challenging undertaking, given that some former students cannot read, are not comfortable speaking English or French, live in remote locations or are deceased.

Advocates for the destruction of the documents argue that the highly sensitive stories were told under the assumption of secrecy.

Former Assembly of First Nations leader Phil Fontaine told the Ontario court that stories of aboriginal-on-aboriginal abuse at the schools could prove damaging to First Nation communities.

Mr. Moran said those privacy concerns can be addressed through the "rigorous" redaction of sensitive information.

"Everybody, I think, is highly attuned to the fact that these are some of the most personal and hurtful memories that people carry in their lives and we have to be incredibly sensitive and respectful of the potential for harm that can be created from this. But does that have to come at the complete and total expense of destruction? My hope and my feeling is that it probably doesn't."