WASHINGTON—An appeals court late Wednesday granted the Justice Department’s request to retain control of the classified materials seized at former President Donald Trump’s Mar-a-Lago resort and continue its criminal investigation into the handling of those documents, in a big win for the government. In a 29-page decision, the 11th Circuit U.S. Court of Appeals in Atlanta lifted an earlier order from a federal judge who had barred federal agents from using roughly 100 classified documents seized as part of its probe into whether any national-security risks had been posed by the way the highly sensitive government material was being held at Mr. Trump’s Florida home.

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