There is no contradiction.
Virginia had forfeited its rights in the making of federal law and had pulled its members out of the Congress. The people of WV remained in the Union no matter what the Slavers wanted.
The secession of West Virginia still stands as a glaring example of northern hypocrisy on the issue itself. You say states cannot secede yet the north acted as though they did secede by allowing West Virginia to break away from it's union with the state of Virginia WITHOUT the citizens of the entire state of Virginia having a say in the matter. To politically honor the act of the first secession by allowing the second secession to proceed is exactly what they did.
If a state cannot secede is your position then Virginia never legally seceded in the first place. If this is the case, the state of West Virginia would not have been allowed to stand.