In Federally occupied Tennessee, Robert Looney Caruthers, a Democrat, was never inaugurated, as Andrew Johnson, a Unionist, was appointed military governor.
Edit - I assume you mean William "Extra Billy" Smith. He was elected Governor of Virginia in 1863, took office on Jan. 1, 1864, and served to the end of the war, so he was not prevented from being inaugurated.
ROBERT LOONEY CARUTHERS was born in Smith County, Tennessee. Educated at Washington College, he studied law and served as circuit attorney general from 1827 to 1832. He was elected to the state legislature in 1835 and to Congress in 1841. Twelve years later he was appointed to the state Supreme Court by Governor William Campbell. He went on to serve as a member of the Peace Congress in 1861. Although elected governor in 1863, he was never inaugurated due to the fact that Andrew Johnson was appointed military governor by Abraham Lincoln. An advocate of education, Caruthers and his brother co-founded Cumberland University Law School.
"On July 17, 1863, the state's Confederate leaders met in Winchester, Tennessee, and nominated Caruthers for governor to replace Isham G. Harris,[11] who was prohibited by the state constitution from seeking a fourth consecutive term.[10] Caruthers was officially elected on August 6,[11] but the state constitution required that the governor-elect take the Oath of Office before the General Assembly. Since the Union Army controlled most of Middle and West Tennessee at this time, the Assembly was unable to convene, and Caruthers never officially took office. Confederates continued to recognize Harris as governor until the end of the war. Union forces, in the mean time, had installed Andrew Johnson as military governor.[10]" https://en.wikipedia.org/w/index.php?title=Robert_L._Caruthers&oldid=843336858
That's Robert Looney Carruthers. He was elected governor of Tennessee in 1863 but never took office. Future Vice President Andrew Johnson was the appointed military governor at this time.
Tennessee Governor Robert Looney Caruthers (July 31, 1800 – October 2, 1882) On July 17, 1863, the state's Confederate leaders met in Winchester, Tennessee, and nominated Caruthers for governor to replace Isham G. Harris,[11] who was prohibited by the state constitution from seeking a fourth consecutive term.[10] Caruthers was officially elected on August 6,[11] but the state constitution required that the governor-elect take the Oath of Office before the General Assembly. Since the Union Army controlled most of Middle and West Tennessee at this time, the Assembly was unable to convene, and Caruthers never officially took office. Confederates continued to recognize Harris as governor until the end of the war. Union forces, in the mean time, had installed Andrew Johnson as military governor.[10]
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I believe it was former Gen. Allen of Louisiana; of course the state capital Baton Rouge was in Federal hands from 1862 on.
Edit - Henry Watkins Allen was elected in 1863, took office in 1864, and continued to serve until the collapse of the Confederacy. Though the Union controlled a good bit of Louisiana, it was not able to prevent his inauguration.