What is Virginia had not seceded from the Union? Would this have affected the war? Why or Why not?

Yes it would have because if Virginia had rejected secession, the prospect of Lee in command of Union forces rather than Confederate forces would have presented major problems for the Confederacy. The South would have lost a major economic and political asset, the state of West Virginia would never have been created, the war would almost certainly have been shorter. Interestingly, such circumstances might cast some doubts on how determined the North would have been to end slavery permanently.
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Yes the capitol of the confederacy was in Virginia mainly for incentive for Virginia to leave the union. Without Virginia the confederacy would be lacking in a major ammount of funds and man power as well as territory

The answer is forindependence.