In new court papers, Army officials have acknowledged that the lead prosecutor in the court-martial of a brigadier general accused of sexual misconduct believed that the most serious charges would be “very difficult to prove at trial” because of questions about the credibility of the main accuser, a junior officer. But the officials said they did not doubt the woman’s central claim that the general forced her to perform oral sex on him while they were serving in Afghanistan.

The lead prosecutor, Lt. Col. William Helixon, abruptly resigned from the case two weeks ago, throwing the prosecution into turmoil near the start of the trial, which is scheduled to open on Tuesday at Fort Bragg, N.C. Lawyers for the general, Jeffrey A. Sinclair, asserted at the time that Colonel Helixon shared their belief that the prosecution’s chief witness had lied on the stand at a January pretrial hearing and that the main charges should be dismissed.

In the new court papers, the Army confirmed the defense team’s assertion that Colonel Helixon had told them that the sexual assault charges should be dismissed, and that he had recommended that more senior officers consider accepting General Sinclair’s offer to plead guilty to lesser charges. But the papers say that the problematic testimony was unrelated to the accuser’s central claims, and that Colonel Helixon did not question that the sexual assault had occurred.

General Sinclair, a former deputy commander of American forces in southern Afghanistan, is one of the highest-ranking officers to face court-martial in recent decades. If convicted of the most serious charges, he could face life in prison and permanent registration as a sex offender.