West Virginia - why didn't they rejoin rest Virginia?

Quite. There were military operations in what is now West Virginia throughout the Civil War. But taking it back, and then making the ongoing effort of holding it, was not a priority for the Confederacy, beset on so many other fronts.

The short answer is they had their hands full just holding on to the rest of the state, and in particular protecting Richmond. They did control parts of West Virginia at times, but it was mountainous, hostile, and surrounded on three sides by Union territory. Their resources were better spent on holding areas that actually wanted to be part of the Confederacy.

There’s also the detail that West Virginia is pretty mountainous, and invading mountains is not easy - see Switzerland and Afghanistan. Maybe if Virgina wasn’t helping to fight the Civil War they could have invaded West Virginia but doing both at once just wasn’t doable.

The beautifully situated town of Harper’s Ferry, West Virginia, changed hands eight times during the Civil War. (It’s really worth a visit.)

Mostly, the Army of Northern Virginia had other things to do.

Robert E Lee’s first battle in the Civil War was at the Battle of Cheat Mountain in September 1861 in what is now West Virginia. He lost because as mentioned attacking in mountainous territory is difficult. The Confederacy was divided on whether it should defend all its territory or form defensible borders.

There were actually some significant efforts during the war to obtain control of West Virginia. The area has a goodly concentration of salt mines, and salt is like really important to have. But the rebel forces lost their only truly concerted effort at invading and controlling the trans-Allegheny region in 1861.

On the main question:

The creation of West Virginia was authorized on behalf of Virginia by the “Restored Government of Virginia”, which met in Wheeling, VA (now WV) until 1863, at which point it moved to Alexandria, by then firmly in the hands of the Union forces. As Colibri points out, they were primarily from the part of Virginia that became West Virginia (though not all were), and they existed in large measure for the purpose of fulfilling the requirement of Article VI of the Constitution. After the formal creation of West Virginia (6/20/63), the Restored Government claimed control over those parts of Virginia in Union control. It moved to Richmond in 1865, though by that time, the Governor selected by the Restored Government (Gov. Pierpont) had been appointed Provisional Governor of Virginia by President Johnson.

When Virginia was re-admitted to the Union, one of the conditions of re-admission was that its new constitution explicitly ratify the creation of West Virginia. This was at the insistence of the radical Republicans who controlled Congress. The 1869 constitution did exactly that, ending any chance of a legal challenge to the creation of West Virginia.

That’s truer now than it was in the past. States used to be able to follow the example of the United States Senate and create unequally populated voting districts.

Let’s use New York as an example. Suppose the state constitution said that each county was entitled to send two representatives to the State Senate. The eight counties in the NYC region (NYC plus Long Island and Westchester) make up 61% of the state’s population. But the sixteen Senators from those counties would be vastly outnumbered by the one hundred and eight Senators representing the rest of the state.

This sounds extreme but this kind of unequal representation was actually pretty routine until the Reynolds v Sims decision in 1964.

I believe that the Confederate Constitution allowed for states to secede from the CSA. That, after all, is what they were fighting about.

I dont think so.

Indeed,I was mistaken.

The Confederates believed that the US Constitution itself implicitly gave states the right to secede. Explicitly spelling that out in the CSA Constitution would’ve undermined that argument.

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Well, the Confederates also believed that the U.S. Constitution implicitly guaranteed their right to travel with their slaves throughout the federal union without having their slaves suddenly become free when they crossed the state line (see the Dred Scott decision), but they made sure to spell that out in their new constitution:

They also believed that the correct interpretation of the U.S. Constitution would be that Congress had no power to bar slavery from the territories (again, see Dred Scott), but they also made that explicit, regardless of whether or not that might have undermined their pre-war arguments:

Which is a really poor source. AIUI, it was written by someone(s) who’d never been in WV and the geographic features it mentions (Shenandoah River, Blue Ridge Mountains) are almost entirely in other states.