In an unusual move, Mr. Bove insisted that the prosecutors appeal the ruling to a district court judge, these people said. After weighing the request, Judge John G. Koeltl of Federal District Court of the Southern District of New York instructed the chief magistrate judge, Sarah Netburn, to reconsider the application, the people said.
But the second time, the government lawyers fared even worse. Judge Netburn not only rejected the request for a search warrant, but she also ordered the government to abide by a special condition: Should prosecutors ever try to refile such an application before another federal judge, they had to include a transcript of the sealed discussions in her court, these people said.
Part of the judge’s skepticism, these people said, stemmed from the absence from the case of lawyers with the Manhattan federal prosecutor’s office. But prosecutors in the Southern District of New York were wary of signing onto the effort and had minimal involvement with it, these people said. A spokesman for the U.S. attorney’s office in Manhattan declined to comment.
While civil rights prosecutors conducted the investigation that Mr. Bove had demanded, they often pushed back against specific steps that he wanted taken, these people said, arguing that they were either not justified by the available facts or contrary to law and past practice, or both.
At one point, Mr. Bove instructed F.B.I. agents on the joint terrorism task force in New York to put on their raid jackets, go to Columbia’s campus and stand in a phalanx near any protesters. Within the civil rights division, the instruction was viewed as deeply improper and a blatant attempt to intimidate students, these people said. The F.B.I. agents did not make any such show of force.
By early April, the investigation seemed to have largely died, but nothing prevents Mr. Bove or others from reviving it. In its wake, however, people familiar with the case said it had only exacerbated the ill will and distrust between political appointees at the Justice Department’s headquarters in Washington and the prosecutor’s office in New York, as well as between those political appointees and veterans of the civil rights division.