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

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

General Sinclair, 51, who was recalled in 2012 from his job as deputy commander of American forces in southern Afghanistan, has acknowledged a three-year affair with the witness, a military intelligence officer who worked for him. But he has denied her accusation that he forced her into oral sex and threatened to kill her and her family if she told anyone about the affair.

The general faces additional counts of misconduct based on the testimony of other prosecution witnesses — including accusations that he pressured a 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, General Sinclair could face a life sentence.