A federal judge ordered the State Department on Thursday to work with the FBI to get access to the 32,000 emails former Secretary of State Hillary Rodham Clinton said were personal and that she didn’t return to the government, as the courts get more deeply involved in the Democratic presidential front-runner’s email practices.

One judge is trying to decide how the government is going about determining what classified information is included in Mrs. Clinton’s messages, while another is exploring the email practices of Mrs. Clinton’s top aides, as the State Department deals with a backlog of requests for her communications, which she only recently returned to the administration.

Responding to a judge’s order, the State Department instructed Mrs. Clinton and aides Huma Abedin and Cheryl Mills to save all “federal documents, electronic or otherwise, in her possession or control,” and to assure the government that none of them will be deleted.

Those instructions were sent Aug. 10 — a day before Mrs. Clinton announced through her campaign that she would turn the server she used for email during her time as secretary over to federal investigators, who were already looking into whether classified information was being stored in an insecure manner on the server or a flash drive held by her personal lawyer.

Lawyers for both Ms. Abedin and Ms. Mills responded with assurances their clients would not destroy any documents, while David E. Kendall, Mrs. Clinton’s lawyer, only assured the State Department she wouldn’t delete any emails she deemed federal records.

She has already turned over those messages, though she said she has deleted about 32,000 other emails from her time in office that she deemed purely personal.

Judge Emmet G. Sullivan, in a case brought by Judicial Watch, ordered the State Department, which is supposed to be the custodian of her records, to talk with the FBI to see what of those emails it could obtain from the server.

Judicial Watch, a conservative public interest law firm, has been trying to get a peek at Mrs. Clinton’s communications for years, but was unknowingly foiled by her email practices, in which she issued herself her own account on a server she kept at her home in New York rather than using the State Department’s usual system.

Prodded by the House Benghazi review panel, the State Department belatedly admitted Mrs. Clinton had never allowed her records to be part of the usual record-keeping system, and so they were never checked when Congress or others examined her communications.

Nearly two years after she left office, Mrs. Clinton returned the records to the department, which has now spent eight months trying to process them, and has released several thousand out of 55,000 total pages.

Those 55,000 pages, comprising about 30,000 emails, were the ones Mrs. Clinton deemed to be government business and returned to the department. She said there were about 32,000 other messages that were entirely personal, which she didn’t turn over. She said she has since expunged all of the messages from the server, so it’s not clear what records can be retrieved by the FBI and State Department.

Tom Fitton, president of Judicial Watch, said the group is asking the courts to insist that the State Department play a more active role in seeing whether Mrs. Clinton made the right calls in deciding which records she deemed government business and which she deemed private.

“It’s not clear they’ve turned over all of Mrs. Clinton’s records,” he said.

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