There are two cases, just discussed, which reflect on the ability of the Congress to "ratif[y] what ha[d] been done." Congress both ratified Lincoln's emergency suspension and authorized additional suspensions by the President. Ergo: Lincoln's habeas suspensions, even if "extralegal" at the time (which I do not concede), were validated.
...the main problem, of course, being the two years of intervening time between the suspension and Congress' act during which five separate federal court orders were disobeyed.
I suppose that you could make the case that Congress indemnified Lincoln from those previous five cases over the previous few years, but indemnification by its very definition would function by removing the legal penalties he would otherwise face in its absence. That would constitute a law that "renders an act punishable in a manner, in which it was not punishable, when it was committed," which of course is the Supreme Court's landmark definition of an unconstitutional Ex Post Facto law from Fletcher v. Peck (1810).