You misunderstand the Habeas Corpus Act of 1863, and intentionally misrepresent it. Historian Phillip Shaw Paludan, writing about the 1863 Act:
"Conscription was clearly on their minds as lawmakers wrote the Habeas Corpus law (1862-1863). The Militia Act of 17 July 1862 had been followed quickly by an executive proclamation that suspended the writ to allow arrest of anyone running from or interferring with the draft provisions of the law. Conservative state judges had been accepting writs to protect men from such suspension and from confiscation of propoerty as the Union Army moved south. These suits often charged federal officials with violation of state trespass, false arrest, or libel laws.
"The Habeas Corpus Act gave immunity to federal officials acting under presidential suspension and allowed cases to be removed from state to federal courts when defendent soldiers faced state accusations. It was an important provision for the future. At the conclusion of the war, thousands of suits would be launched in the defeated Southern states suing Union soldiers and officials for allegedly unlawful seizure, destrcution of propoerty, or deprivation of liberty. The law would protect victorious Unionists form rebel vengeance."
What Paludan indicates here, and as I stated in the now-deleted 4000+ post thread, was that it took Congress some time to reach the final legislation. Your interpretation of the terms of the Habeas Corpus Act are wrong.
Section 1 of the Act empowered the President to suspend (the privilege of the the writ of) habeas corpus for so long as "said rebellion continue." It orders judges and courts to suspend habeas proceedings for any person held under the Presidnet's authority, "whenever and whereever.". That is a key point you ignore - those already held fall under the provisions.
Sections 2 and 3 amplify Section 1. Those who have been detained who are not prisoners of war ("state or political prisoners") can still be detained. The Sec. of State and Sec. of War were to provide lists of names of those detained. If they had not already been indicted, they could be released upon oath and/or bail, and failure to take the oath or post the bail meant that they continue to reside in custody. The effect was to release the minor offenders.
Section 4 again refers to the entire ACW, not just "from this time forward." It begins with the clause, "That any order of the President, or under his authority, made at anytime during the existence of the present rebellion ..." The thrust of the legislation was to recognize and ratify the President's actions until congress could make its political decision.
NC is correct. Congress killed Lincoln's attempts for a habeas corpus law for two whole years. A Federal court made note of this fact in September 1862 when yet another habeas corpus case was decided against Lincoln:
When the counsel for the petitioner, some days since, suggested that he desired to apply for a writ of habeas corpus to bring up the body of the petitioner, I had the impression that congress, at its last session, had passed an act authorizing the president to suspend the writ of habeas corpus, and that he had sanctioned the order of the war department under such authority. If this had been the case, I should have held it to be my duty to refuse a writ, in a case within the scope of the law of congress, and the order of the president; but having, since that suggestion was made, received the acts of the last session, I find that I was mistaken, and that congress has passed no law on this subject. The question of the power of the president to suspend the privilege of habeas corpus, without the authority of congress, is therefore presented in this case, if the order of the war department is deemed to be the order of the president, and to extend to such a case as that now under consideration. (Ex Parte Benedict, 1862)
Our conclusion is, that no much of the 5th section of the act of Congress, March 3d, 1863, entitled 'An act relating to habeas corpus, and regulating proceedings in certain cases,' as provides for the removal of a judgment in a State court, and in which the cause was tried by a jury, to the Circuit Court of the United States for a retrial on the facts and law, is not in pursuance of the Constitution, and is void.
If you look at HR 591, as recorded on Dec 9, 1862, the working title was "An Act to indemnify the President and other Persons for suspending the privilege of the writ of Habeas Corpus and acts done in pursuance thereof." It also came with a preamble which explained the reasons for the proposed Act:
The Indemnity Bill was passed on March 3, 1863.
8. In using the name "Indemnity Act" to designate the law of March 3, 1863, contemporary usage has been followed. Senator Trumbull and others referred to the measure while under debate as the "Indemnity Bill," and the same designation appeared in the heading of the record, as well as in many other places. (Cong. Globe, 37 Cong., 3 Sess., pp. 1459, 1479.)
Source: James G. Randall, Congressional Problems Under Lincoln, Revised Edition, (1951), p. 189, fn 8.
1863.THE CONGRESSIONAL GLOBE.
INDEMNITY BILL.
The SPEAKER. The hour of one o'clock having arrived the vote will now be taken, by previous order of the House, on agreeing to the report of the committee of conference on the indemnity bill
Mr. ALLEN, of Ohio, called for the yeas and nays.
The yeas and nays were ordered.
The question, was taken; and it was decided in the affirmative-yeas 99, nays 44; as follows:
* * *
Source: Congressional Globe, 37th Congress, 3rd Session, March 2, 1863. (Page 1479)
The Indemnity Bill of March 3, 1863 did not ratify any previous acts.
As Senator Trumbull, a sponsor of the Indemnity Bill, explained: "We do not propose to say that suit shall be dismissed, that a proceeding is null and void, but we propose that certain facts shall be a defense to an action." (Cong. Globe, 37 Cong., 3 sess., p. 1436.)
Had the unconstitutional suspensions been ratified, there would be no cause of action.
Here is what historian Paludan says, cited to an actual book, with page number.
State governments earned the respect of their citizens by energetic efforts to protect state regiments and support the war. They demanded the respect of the federal government by jealously upholding their rights in state courts. When Congress passed the 1863 Habeas Corpus Act, it had inserted a provision which provided protection from prosecution for federal officers performing military duties. In state after state, judges either struck down the measure or evaded it and asserted the traditional lineaments of the federal systern. Despite a war for Union and against the ultimate assertion of state sovereignty, state judges insisted on affirming their own prerogatives. The Union they envisioned was a union of states. Before the Democratic party had adopted the slogan "The Constitution as it is, the Union as it was," state judges had insisted on the slogan as a fact. [18]Perhaps the most revealing explanation of states' rights feeling came from Illinois Governor Yates in January, 1865. Yates was a militant radical in the Reconstruction era and anticipated such sentiment before Appomattox. During the war he was most vigorous in urging greater effort by the federal government against the rebellion. He led the way in demanding the radical step of using black troops as combatants. Yet such beliefs did not preclude a marked commitment to preserving state influence and integrity.
There was, he told the state assembly in January, 1865, no "political heresy so dangerous to our existence as the doctrine of the right of secession." But it was dangerous because it was similar to ideas rightly cherished by Americans everywhere. Southerners had taken the poisonous doctrine of secession and "sugar coated [it] with the plausible sobriquet of State Sovereignty." Beguiled by the southern view of what constituted such sovereignty, unprincipled Northerners had attempted to inhibit the ability of the government to preserve itself.
That did not mean that state sovereignty was in itself wrong. After all, Yates explained, the motto of Illinois was "State Sovereignty and National Union." When understood properly, this was "the best and most beautiful motto which adorns the armorial bearing of any state in the Union." He continued:
I am for unlimited state sovereignty in the true sense, in the sense that the State is to control all its municipal and local legislation and I would be the first to resist all attempts upon the part of the Federal Government to interpose tyrannical usurpation of power in controlling the legislation of States. The States are sovereign in every sense in whcih it is desirable they should have sovereignty.... [19]
[18] The state cases are Griffin v. Wilcox, 21 Indiana 370 (1863); In re Kemp, 16 Wisconsin 382 (1863); Warren v. Paul, 22 Indiana 276 (1864); Short v. Wilson, 1 Bush 350 (1866), (Kentucky). Randall (Constitutional Problems, 428-429) describes as "frequent" cases where federal officers were held answerable by state courts despite the 1863 bill.
[19] Reports Made to the General Assembly of Illinois, 34th sess. (Springfield, 1865), I, 28; Edward Gambill, "Who Were the Senate Radicals?" Civil War History, XI (Sept., 1965), 237-244.
Source: Phillip S. Paludan, A Covenant With Death, 1975, pp. 33-35.