From what little I have seen in records the answer is that they didn't straighten them out. The new state government did.
With the advent of the Occupiers and Carpetbag governments the first thing that the new government did was to demand that the property taxes for 1861 to 1865, that the people had paid to the Confederacy, were to be paid again to the new federalist state government, as back taxes, in US currency.
Well you can see what kind of solution that would be. Very few people could paid such an amount of "back taxes" after 4 years of war. This inability to pay these taxes and abandoned property of the people who had moved off, became a land redistribution program and was how the Government got the property for the Freedmans Bureau "40 acres and a mule" programs. The large amounts of realitive cheap lands were also quickly taken up by land speculators and profiteers. Of course because most of the Freedman who recieved the "40 Acres" had little or no mangement skills, that land again became abandoned or lost due to inability to paid their yearly taxes also.