'In the autumn of 1867 Mr. O'Conor, after incessant efforts, aided by men of all parties succeeded in getting a time appointed for the decision of Mr. Davis's case, either for trial or a nolle prosequi, but both would have preferred the former as a test question. As winter drew on Mr. Davis was summoned to Richmond, but the nolle prosequi was filed.'
From Bouvier Law Dictionary Rev. 6th ed. (1856), NOLLE PROSEQUI, practice. An entry made on the record, by which the prosecutor or plaintiff declares that he will proceed no further.
The federal government abandoned the case, not Davis. Specifically, due to the complete pardon by Johnson 25 Dec 1868. A pardon that Jefferson Davis did not want.
'If my opinion is worth anything, you can ALWAYS say that few people could have done better than Mr. Davis. I knew of none that could have done as well.' - R. E. Lee
"Thus, Davis still faced a charge of treason. At court in Richmond, Chief Justice Chase finally joined Judge Underwood on the bench. In the mean time, the Fourteenth Amendment to the Constitution had been ratified by the states and had gone into effect on July 28. Its third section stipulated taht no person could hold office who had sworn an oath to uphold the Constitution and subsequently had participated in the rebellion. To Chase this provision offered a way around the morass of a Davis trial because there could be no double jeopardy. In conversation with George Shea, Chase made clear his viewpoint.
"Chase's opinion dictated the strategy of the Davis defense. Davis's lawyers readily admitted that in 1845 he had taken an oath to support the Constitution. They submitted a motion asking that they indictment be quashed on the grounds that the 14th Amendment had already inflicted punishement on their client. The government's attorneys contested the point. The chief counsel, Richard Dana, countered that the Constitution was not criminal law...On December 5 the court handed down a divided ruling. Chase stated that he and Underwood could not agree. He accepted the arguement tendered by the defense; Underwood rejected it. Counsel for the defense requested that the facts of the disagreement be certified to the Supreme Court. Chase so ordered. As the indictment remained in force, the federal attorney wanted a trial date set. Chief Justice Chase saidn the date could be announced after the completion of the upcoming Supreme Court term.
"William Evarts, who had become U.S. attorney general in July 1868, decided the government would push no further." -- "Jefferson Davis, American" by William J. Cooper, Jr. pp 581-582
Looks like Davis' attorneys jumped at the chance to avoid a trial.
But Davis' counsel moved to drop the charges on 14th Amendment grounds weeks before Johnson issued his pardon. They were not anxious to take the case to court because they saw no reason to participate in Davis' quest for martyrdom. They knew better than Davis did that a trial could result in years in prison.