In areas of the Confederacy dominated by Union troops, President Abraham Lincoln desired the establishment of pro-Union, state governments. That meant that some southern states had both a Unionist government and a Confederate government, often times in exile.
The establishment of pro-Unionist governments depended on Federal forces enrolling pre-war Unionists, those who had opposed the secession of the South; Lincoln saw those individuals as the core of any pro-Unionist state government and opposed the inclusion of any were unwilling to take an oath of allegiance to the United States.
On Sunday, January 31, 1864 Lincoln once again expressed his views to General Nathaniel Banks in Louisiana, instructing Banks that he was “at liberty to adopt any rule which shall admit to vote any unquestionably loyal free state men and none others.”