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In the book “Lee: The Last Years” by Charles Bracelen Flood he notes that none of the southern leadership, including Lee, was ever tried for treason. He says that Salmon P. Chase, who was then Chief Justice, told Federal Prosecutors to not try it because they might not get a conviction and that would set a bad precedent.

I have actually ran across quoted bits of this discussion, and if memory serves me right, I believe what Justice Chase said was "You will lose everything in the courtroom that you gained on the battlefield."

I have only listened to the audiobook and am going from memory. As a recovering academician, I keep meaning to be diligent by checking sources. That means getting a print copy of Flood’s book for his exact quote and then checking Flood’s citation to exactly what Chase said and then looking that up for Chase’s original words. Until then, I’ll go with your version. Thanks!

DiogenesLamp: "I have actually ran across quoted bits of this discussion, and if memory serves me right, I believe what Justice Chase said was "You will lose everything in the courtroom that you gained on the battlefield.""

Several things need to be pointed out here:

Chase was a fickle politician, a RINO, similar to some today, he served as Lincoln's Secretary of Treasury during the Civil War, then switched parties and ran for the Democrat nomination for president after the war.
Chase's words, if accurate, are obviously true considering that Davis would have been tried for treason in Richmond, VA!!
It would be like today, John Durham trying to get convictions for anti-Trump conspirators in Washington, DC!
Not going to happen.
Had such a trial been held in, for example, Boston, then Davis's conviction would be a near certainty.
Chase was convinced Davis's best defense would be that he forfeited U.S. citizenship upon secession, and therefore could not have committed treason.
In 1868, Chase himself dismissed treason charges against Jefferson Davis based on the argument that the new 14th Amendment prevented further punishment of former Confederates.

So, arguments over alleged Confederates' treason are strictly theoretical, hinge on whether you consider Confederates to have legally left the Union, which no Congress or Supreme Court ruling ever did, but which Democrat Chase himself was willing to contemplate.
However, that was not the argument which Chief Justice Chase used to dismiss treason charges against Jefferson Davis.
Rather, Chase said, in effect, "Davis has already been punished enough, no double jeopardy for Confederates."

Chief Justice Chase hatched the idea, and presented it to the defense ex parte, to present a motion to drop the prosecution on a 14th Amendment argument. The 14th imposed a penalty on those who had sworn an oath to support the Constitution and had then engaged in insurrection or rebellion. Any subsequent prosecution for the same acts would be double jeopardy. And that was legal reasoning of how the government got out of bringing the case to trial, while not losing face.

The following may be of interest in determining why the prosecution did not want to proceed. Evarts was the lead prosecution attorney and, following the withdrawal of John Clifford, the only one of substantial note. He brought on Richard H. Dana to add some much needed heavyweight lawyering. The correspondence of Dana to Evarts provides significant insight.

Richard H. Dana, Jr. and William M. Evarts to Henry Stansbery, February 26, 1868, draft letter by Dana, at request of Evarts, never sent to Stansbery.

Our minds have been moved from the first by doubts of the expdiency of trying [Davis] at all which have so ripened into convictions that we assume the reponsibility of offering to you unasked, our opinion upon th subject. … We cannot see any good reason why the government should make a question whether the late war was treason and submit it to the decision of a petit jury of the vicinage of Richmond… The legal issue was whether secession by a state was a constitutional right which made legal what would otherwse have been treason.… we feel also assured that the public interest in this trial has very much abated, if not ceased. And as to the direct result of a conviction, the sentence of death for Mr. Davis, we suppose we shall have your concurrence when we express our belief, that after this lapse of time and all that has occurred in the interval, the people of the United States will not desire to see it carrried into execution… In short, we feel it our duty to suggest to you the consideration in which we cannot but think you will concur, that the point of law which the government can desire to have mooted and ruled upon, is one already sufficiently settled, and that the only matter of fact to be submitted to the jury is one of those events of history to which no doubt can ever be attached. Under such circumstances we cannot but think that the dignity of our republic will be lowered and the adequacy of our political system to deal judicially with such cases brought into doubt, by making a question of the law and of these established facts, and putting the power of any one man on a petit jury, at Nisi Prius, to give a triumph to the chief traitor and his favorers, and a defeat to the government which will not be much the less humiliating because it will be absurd.

Richard H. Dana, Jr. to AG William M. Evarts to August 24, 1868.

Sir,
While preparing with yourself, before you assumed your present post, to perform the honorable duty the President had assigned to us, of conducting the trial of Jefferson Davis, you know how much my mind was moved, from the first, by doubts of the expediency of trying him at all. The reasons which prevented my presenting those doubts no longer exist, and they have so ripened into conviction that I feel it my duty to lay them before you in form, as you now hold a post of official responsibly for the proceeding.
After the most serious reflection, I cannot see any good reason why the Government should make a question whether the late civil war was treason, and whether Jefferson Davis took any part in it, and submit those questions to the decision of a petit jury of the vicinage of Richmond at "nisi prius".
As the Constitution in terms settles the fact that our republic is a state against which treason may be committed, the only constitutional question attending the late war was whether a levying of war against the United States which would otherwise be treason, is relieved of that character by the fact that it took the form of secession from the Union by state authority. In other words the legal issue was, whether secession by a State is a right, making an act legal and obligatory upon the nation which would otherwise have been treason.
This issue I suppose to have been settled by the action of every department of the Government, by the action of the people itself, and by those events which are definitive in the affairs of men.
The Supreme Court in the Prize Cases held, by happily a unanimous opinion, that acts of the States, whether secession ordinances, or in whatever form cast, could not be brought into the cases, as justifications for the war, and had no legal effect on the character of the war, or on the political status of territory or persons or property, and that the line of enemy's territory was a question of fact, depending upon the line of bayonets of an actual war. The rule in the Prize Cases has been steadily followed in the Supreme Court since, and in the Circuit Courts, without an intimation of a doubt. That the law making and executive departments have treated this secession and war as treason, is a matter of history, as well as is the action of the people in the highest sanction of war."