From the Federal perspective, it gave authorities some point of reference as to who was a former soldier and who might be a guerilla. The Official Records contain a number of interesting accounts concerning guerilla bands and their leaders, who were sometimes hunted down and killed -- no imprisonment or trial.
As far as paroles for soldiers surrendered with Johnston in North Carolina, most people probably don't know where to look. Take for example soldiers of the 46th Alabama Regiment. Some took the oath of allegiance as a condition of release from prison. Others who happened to be detailed or home on furlough or those who had simply given up and gone home were included with Taylor's surrender and could have received paroles under the Citronelle agreement. Those paroles with be found with each soldier's military file, as you would normally expect.
Expections will be found among members of the 46th Alabama who went to North Carolina.
On April 9, 1865, survivors of Companies “D” and “K” merged with others from the 31st Alabama Regiment to become Company “A” of the consolidated 19th Alabama Regiment. Companies “A” and “H”, “E” and “F”, “B” and “I” were paired to form Companies “A”, “B” and “F”, respectively, of the consolidated 23rd Alabama Regiment. These commands surrendered at Salisbury NC, May 2, 1865. Paroles for these officers and men will be found with the 19th and 23rd Alabama Regiments.