After reading that post Rafki, I am somewhat wondering if the following should be done...
Remove the Army of the Potomac HQ under Beauregard.
Create the Army of the Shenendoah HQ under Johnston.
Since the AotP changed into a corps of the new AoNV, I basically see things as the Army of the Shenendoah 'merged' with the Army of the Potomac and changed into the Army of Northern Virginia. Either HQ represented would be 'valid'.
This might aid the process of the game's transition of HQ commanders, since Beauregard will be a Corps commander, and Johnston the Army commander (not vice versa).