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The military’s most closely watched sexual-misconduct case was thrown into turmoil after the Army’s lead prosecutor abruptly left the case less than a month before the scheduled court-martial of Brig. Gen. Jeffrey Sinclair on sexual-assault charges.

The departure of Lt. Col. William Helixon this week came days after defense lawyers said in interviews that he had told them he had come to think a jury would not believe the testimony of the prosecution’s chief witness, a 34-year-old captain.

Sinclair, 51, who was recalled in 2012 from his job as deputy commander of U.S. forces in southern Afghanistan, has acknowledged a three-year affair with the witness, a military-intelligence officer who had worked for him.

But he has denied her accusation that on two occasions he forced her to perform oral sex and threatened to kill her and her family if she told anyone about the affair.

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The general faces additional counts of misconduct based on the testimony of other prosecution witnesses — including accusations that he pressured a female subordinate to send him naked photographs of herself — in a case that has become a lightning rod for critics who say the military has played down sexual assault in the ranks. If convicted of the most serious charges, Sinclair could face a life sentence.

Only a few generals have faced court-martial in recent decades, legal experts say.

Maj. Crystal Boring, a spokeswoman at Fort Bragg, N.C., said in an email that Helixon voluntarily left the case for “personal reasons.” Sinclair was a commander with the 82nd Airborne Division at Fort Bragg before being placed on limited duty because of the criminal investigation.

For several days, The New York Times had been putting questions to Army officials at Fort Bragg and the Pentagon about what defense lawyers described as Helixon’s misgivings about the case and his efforts to persuade superiors to drop the most-serious charges.

According to the defense, Helixon also said he believed the captain had not told the truth during testimony at a pretrial hearing last month.

It was impossible to confirm the defense team’s description of conversations with Helixon, who did not respond this week to emails or to messages left at his office and on his wife’s cellphone. Army officials at the Pentagon declined to comment.

Boring declined to discuss other aspects of the case or whether the military would seek to delay the court-martial, scheduled for early March. She said prosecutors would “continue to pursue resolution of these charges,” and added that personnel changes were common in lengthy cases.

If it turns out the prosecutor’s departure stemmed from disagreement about how the case should be handled, that would be “highly unusual,” said Eugene Fidell, who teaches military justice at Yale Law School.

“It’s possible the prosecutor was removed,” Fidell said, assuming the account of Helixon’s concerns was accurate. “But more likely, he was extremely uncomfortable with the way things were unfolding and felt an obligation to remove himself from the case because he may have felt he would be put in an untenable position from a professional-responsibility standpoint.”

Sinclair, who is married and has children, has offered to plead guilty to conduct unbecoming of an officer and to adultery, which is punishable under military law, his lawyers say. But they have pressed hard in negotiations against his serving prison time.

The affair began in Iraq five years ago and continued until the accuser discovered emails suggesting the general was not going to leave his wife, defense lawyers say. In a fit of jealousy, they claim, she confessed the relationship to Sinclair’s commander.

The prosecution has painted a different picture, saying that she tried to break off the relationship and then was bullied, threatened and forced into sex by Sinclair.

Greg Jacob, policy director of the Service Women’s Action Network, an advocacy group, said that even without the testimony of the chief accuser, there was significant evidence against Sinclair on other counts. “If you take the most serious charges out, he’s still done plenty wrong to warrant his being punished by the military,” Jacob said.

Richard Scheff, the lead defense lawyer, said Helixon told him he had expressed concerns about the accuser to a superior at the Pentagon, but was told to move forward to trial on the same charges.

“If the Army is changing its view of this case, we welcome it,” he said in an emailed statement. “If not, we remain disappointed that politics, rather than fairness and justice, is driving the decision making.”

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