This map, like so many, is misleading. The areas "lost" by the Confederacy were, in many cases, not occupied by the Union and were occupied and run by the Confederacy. Multi-year, mobile warfare is very hard to depict on a simple, single map.
Two examples: almost all of Mississippi remained under Confederate jurisdiction throughout the war. Vicksburg was lost, but Canton, Jackson, Grenada and Corinth were not. Corinth went in and out of Confederate control, based on whether a Union army wanted to occupy it, but it and its railroads were the base from which Hood attacked Tennessee in late 1864. In Canton, Jackson and Grenada, the Tithe was paid, bridges rebuilt, railroads ran, etc in late '63 and all of '64. But the map shows all this area "lost" in 1862 or 1863.
Second, the path of Sherman to the sea is depicted as "lost." Yet as soon as his raid had passed, Confederate control was re-established and repairs began to be made. The same with Atlanta. Were these areas undamaged? No, but they were under Confederate control.
Additionally, the map shows areas "lost" by year, giving no consideration to when in the year the "loss" took place. Again, Sherman's raid to the sea was in November and December 1864, but the map does not include that end-of-year fact. Northwestern Virginia was not "lost" to the Confederacy until the fall of '64.
The map is convenient, but misleading.