During the civil war were there any Southern senators or congressmen who stayed in congress? If so did they sit on committees and vote?
If the southern states were technically still in the United States, how could the Senate conduct business if there was no quorum?
Did legislation passed during the civil war apply to the southern states after they lost the war?
By November of 1864, the Union had pushed into the south... did those liberated areas send congressmen to the house? Participate in the presidential election?
When the South seceded, almost all of its Congressmen and Senators resigned when their states seceded, much to the satisfaction of the Republicans, who saw large majorities in Congress as Southern Democrats left (Northern Democrats were largely in schism between War Democrats who supported the war while opposing Lincoln's agenda and Copperheads who outright sympathized with the South).
Note that I said most Southerner Congressmen. 10 Southern Congressmen (including five from Virginia, mostly from what became West Virginia) and 1 Senator, Andrew Johnson (D-TN), remained loyal to the United States and, therefore, remained in Congress. In addition, the "Restored Government of Virginia" (what became West Virginia) sent two Senators, who were seated. Johnson would, of course, become Lincoln's running mate when Lincoln ran for reelection in 1864 (under the "National Union Party" line because the name Republican seemed too partisan under the circumstances...the Republican Party reclaimed its name after the war). During the 1861-1863 Congress, Johnson and the ten southern Congressmen served with little question as to their rights to be there.
In addition, how was the entry of West Virginia handled in Congress? Did they have two Senators and a clutch of Represenatitives added?