I'm aware of the habeus corpus suspension - which I would argue was a bit of an extraordinary case as it was drawn into play initially because of the civil war, the capital was difficult to reinforce because of a rail obstruction and Congress could not safely be called into session. Even then, to my knowledge the act only applied to a small area from DC to like Pennsylvania or something. The act was rendered inoperable at the official end of the war and even before that I think all political prisoners taken during that time were released and even offered amnesty so long as they didn't aid the confederacy, which, again given the extraordinary circumstances is a little more understandable (albeit admittedly still very contentious) than the current situation we have now.

What I'm not aware of is Lincoln's criminal/civil immunity outside of this. Do you have any other information on this? It sounds interesting and something I have never heard of. I'd like to learn about it!