Federal prosecutors are in the process of turning over thousands of pages of classified documents to the lawyer for convicted Al Qaeda supporter Jose Padilla.

The discovery process could shed light on the highly secret imprisonment and harsh interrogation of Mr. Padilla, a US citizen, by the US military – treatment that critics say amounted to torture.

The turnover of the documents was disclosed Wednesday in an open-court conference with US District Judge Marcia Cooke, who is preparing to resentence Padilla after the original 17-year sentence she handed down was overturned by an appeals court as too lenient.

A prosecutor did not reveal the subject-matter of the classified documents being turned over, but he did acknowledge that they are being held by the Defense Department.

That fact suggests that the documents relate to Padilla’s three years of confinement without charge at a military prison in South Carolina.

It further suggests that Judge Cooke is allowing Federal Public Defender Michael Caruso to examine the government’s treatment of his client to assist in the process of determining a new sentence.

Padilla was subjected to a full range of harsh interrogation techniques, including isolation, stress positions, and sleep deprivation, according to his lawyers. They have said the ordeal left him mentally disabled. Mental health experts hired by the defense have supported that conclusion.

The government has denied that the military detention caused Padilla any psychological injury. All details about his treatment at the Brig in Charleston have remained highly classified.

Padilla was transferred from the Brig to the criminal justice system in Miami where he was put on trial for allegedly conspiring to provide material support to Al Qaeda and other Islamic militant groups. He and two co-defendants were convicted.

After his conviction, Padilla was housed in a solitary confinement cell on the high security wing of the supermax prison at Florence, Colo.

In 2012, Padilla’s lawyers expressed concern to Cooke about their client’s “mental well-being.” The judge ordered the Bureau of Prisons to move Padilla to the federal lockup in Miami, in part to facilitate visits from his family.

He has been in Miami since late 2012 awaiting a new sentence. The resentencing has been postponed several times since late 2012.

On Wednesday, Cooke set two more conferences, one in March and one in April. She said she expected to be able to set a firm sentencing date during the April conference.

In a brief update to the judge, Assistant US Attorney Brian Frazier said that so far the government has turned over more than 2,500 pages of unclassified documents and 6,000 pages of classified records from the Department of Defense to Padilla’s lawyer.

More than 4,700 classified documents must still be released, Mr. Frazier added. He said compliance could take another two months.

Padilla did not speak during the conference and showed no emotion.

Physically, he was significantly thinner than during his 2007 trial, with deep-set eyes and long dark hair combed back.

He sat at the defense table leaning slightly forward in his chair, with his eyes aimed straight ahead. He wore the standard prison-issued tan shirt and pants. His ankles were shackled in chains that jingled as he walked from the courtroom.

Padilla’s name became first known to most Americans after Justice Department officials announced in 2002 that he had been plotting a radiological “dirty-bomb” attack against the US. (No evidence of such a plot has been presented in court, and the government has never charged Padilla with involvement in such a plot.)

When lawyers began successfully challenging Padilla’s detention in the criminal justice system as a material witness, President Bush designated Padilla an enemy combatant and ordered him into military custody. He was taken to the Charleston Brig for interrogation where he was held incommunicado for months, without access to a lawyer or contact with family members.

Years later, as the US Supreme Court was about to examine the constitutionality of Padilla’s treatment, the Bush administration moved Padilla to Miami to face charges that he conspired to help Al Qaeda.

After his conviction, prosecutors asked that Padilla be sentenced to life in prison.

Cooke rejected the request and instead handed down a 17-year sentence, which was below the guidelines range. The reduction came in part in recognition of the three years Padilla spent in military custody in Charleston.

A three-judge panel of the 11th US Circuit Court of Appeals in Atlanta voted 2 to 1 to overturn Padilla’s 17-year sentence.

The panel majority said Cooke did not give enough weight to Padilla’s prior criminal record (as a juvenile), gave no weight to his future dangerousness, wrongly compared him to criminals who were not similarly situated, and “gave unreasonable weight to the conditions of his pre-trial confinement.”

In a dissent to that portion of the appeals court decision, Judge Rosemary Barkett accused the majority judges of “blatantly substituting its own view for the discretion of the trial judge.”

Judge Barkett rejected all four of the reasons offered by the two majority judges for overturning the sentence. “There is no support in this record for the majority’s stated reasons and thus no support for its conclusion [to overturn the sentence],” she wrote in her dissent.

Barkett said the ruling “impermissibly usurps the discretion of the sentencing judge in direct contravention of clear and unequivocal Supreme Court and Circuit precedent.”