Vast difference between deserting the army and evading capture by the enemy

In fact, after they evaded being captured, many highlanders reformed in Virginia and North Carolina and fought valiantly until the bitter end of the American Civil War. During the summer of 1863, while men were furloughed from Thomas' Legion (a force which consisted of more than 2,500 highlanders), they defended their homes in the Southern Appalachian Mountains and they operated as "Home Guard" and fought bushwhackers and outlaws. O.R., Series IV, 2, 732, O.R., 53, 324 and O.R., Series I, Vol. 32, pt. II, pp. 610-611

The "absentees" from Thomas' Legion, North Carolina's only Civil War legion and it recruited exclusively from the mountains, were even declared deserters. Most, however, returned to Thomas' Legion in December 1864 and at war's end are recorded on rosters and muster rolls. O.R., 1, 49, pt. 1, p. 1048 and O.R.,1, 49, pt. II, p. 309 

Pro-Unionists and conscription opponents (present day draft dodgers) of Tennessee fled daily, crossed the Cumberland Mountains, and joined the Federal army in Kentucky and Ohio. During the fighting in East Tennessee, additional pro-Unionists and conscription opponents fled into Western North Carolina. During General Robert E. Lee's first invasion of the North in September 1862, many vacated their homes while others deserted the army (Robert E. Lee's wife, Mary Custis, is the great-granddaughter of Martha Washington). They strongly believed in a defensive war only; after all, the South is defending their homeland against Northern Aggression. Some adamantly declared that "I do not own any slaves" and they viewed it as “a rich man’s war and a poor man’s fight.” In the North, however, many dodged the draft by paying commutation fees or hiring substitutes, and many Northerners exclaimed that it was "Rich Man's War!" 

On June 20, 1863, with strong pro-Unionist sentiment, western Virginia broke from secessionist Virginia and formed the state of West Virginia. During the secession crisis, Andrew Johnson remained in the Senate even when Tennessee seceded, which made him a hero in the North and a traitor in the eyes of most Southerners. During secession, Johnson was the only Southern Senator that refused to resign. He was born in North Carolina and was a resident of Tennessee. When President Abraham Lincoln was assassinated, Andrew Johnson became the Seventeenth President of the United States (1865-1869).

Some highlanders deserted after they received pleading letters from starving or threatened families, but the numbers are less than some historians proclaim. Unlike the rest of Tennessee, in East Tennessee pro-Unionists outnumbered secessionists two-to-one. Deserters were also defined as a "class in resistance to conscription" (O.R., Series 4, Vol. 2, p. 783). After shutting down the pro-Unionist newspaper Knoxville Whig, some found refuge in the mountains of Western North Carolina (a.k.a. Southern Appalachian Mountains). When General Burnside captured Knoxville, additional conscription opponents and pro-Unionists sought sanctuary in the Smoky Mountains. In defense of the proponents of “Highlander Desertions,” one highlander regiment with perhaps the highest desertion was the 64th North Carolina Infantry Regiment (a.k.a. Allen’s Regiment). The unit had an unusually high desertion rate. However, these numbers only spiked after the April 16, 1862, Confederate Conscription Act which required a three year minimum enlistment. Most of the 64th N.C. Regiment's 12 month enlistment expired just days after the Conscription Act. Furthermore, many from the 64th North Carolina evaded capture during the surrender of the Cumberland Gap and reformed in North Carolina. There is vast difference between desertion and evading capture by the enemy. Unfortunately, some historians don't state the difference. Many historians and writers do not conclude by stating that many deserters returned to military service. (Additional reading: No Soap, No Pay, Diarrhea, Dysentery & Desertion: A Composite Diary of the Last 16 Months of the Confederacy from 1864 to 1865)