I remember reading that nearly 40% of Virginian officers remained loyal to the Union, so what happened to them? Was there a Union 1st Virginia, and so on? Also, did they face difficulty with suspicion and mistrust from command/the administration?
Every state except South Carolina raised at least one unit to serve in the Union Army. That is, units of white soldiers. African American units were raised later in the war by the Federals as well. In Virginia’s case, by present boundaries, the only unit was Loudoun Rangers, two companies of partisan rangers. Other border states like Tennessee were far more divided and had regular regiments. There was also the regular army. The ordinary Unionist could have joined a unit from his home state if he wanted or simply joined one from another state if more convenient.
Several high-ranking southerners remained loyal to the Union, including Winfield Scott. A Mexican War Hero who had been in the army longer than Lincoln and Davis had been alive, Scott was a Bvt Lt. General and Commanding General of the United States Army in 1860. He wanted command of the Union Army to go to fellow Virginian Robert E. Lee, and urged Lee to stay loyal. Scott's opinion that Ft. Sumter could not be reinforced was questioned by the Lincoln administration when he reasoned its abandonment would pacify the remaining slave states, but this was not quite viewed as disloyal, just political.
Scott’s age, failing health, and inability to tolerate George McClellan limited his abilities, and he resigned in November of 1861, though Lincoln asked for his advice from time to time. He died shortly after the war.
George Thomas, another Virginian, served in the Western Theater where he rose to command of the Army of the Cumberland. He had a moderate amount of administrative support, bolstered by his good record. He had been offered command of the Army of Ohio earlier, but declined. After the war, he served on the Pacific coast. Thomas’ younger brother Benjamin apparently forgave him, but his sisters are described as having disowned him, and one is quoted as saying her brother had been dead to her since 1861 on the event of Thomas’ actual death.
John Gibbon, a division commander in the Army of the Potomac, was from North Carolina. Three of his brothers and his cousin Johnston Pettigrew fought for the South. Gibbon, a slave owner, was not particularly happy with the Emancipation Proclamation, writing “if this contest is going to end in an abolition war I cannot remain in the service,” but he stayed it out, as did many men who had said the same thing. He remained in the Army after the war.
Admiral David “damn the torpedoes” Farragut is also sometimes cited because he was born in Tennessee, though his adoptive family (David Porter) was from the north.
As for mistrust from comrades, they seemed to have suffered less than their northern-Confederate counterparts, notably John Pemberton. However, Pemberton surrendered Vicksburg, a move seen as disastrous. Northern origin was another insult in the arsenal.