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Thank you for your great question. I consulted with several of my colleagues throughout NARA and we all agree the records could be held in a variety of Record Groups at the National Archives. Record Groups are the way we organized the collection. They reflect the Federal Agency that created the record. Because the surveys occurred in the South during the Civil War and then the land was distributed through a mixture of ways there are numerous agencies that would be involved.
The first place to start is with the Department of the South, RG 393. A search in our Catalog shows a variety of maps held at the National Archives in Washington, DC and in the Cartographic Section at the National Archives in College Park, MD. You can see the list of series here. I also found a series of records regarding Hilton Head, SC that might be of interest to you. It is described in the catalog here. A larger listing of the RG 393 for South Carolina can be found here as well.
Additionally records might be held under the Army Corp of Engineers (RG 77), the Freedman’s Bureau (RG 105), The Quartermaster General (RG 92), or the General Land Office (RG 49) just to name a few.
My suggestion is that you spend some time looking at the links I sent you from the catalog. If you find a specific document or series that you are interested contact the office that holds it directly. If you cannot find a specific document or series please contact the Archivist in Carto and at the National Archives in Washington, DC. You can reach them at firstname.lastname@example.org or Archives1reference@nara.gov. Please make sure you include the topic of your research in the subject head of your email to make sure it gets to the correct office in a timely manner. Best of luck with your research project.