I recommend contacting the National Archives at Philadelphia directly. The email address is: Philadelphia.email@example.com. You can also visit their website for more information: The National Archives at Philadelphia | National Archives .
Unfortunately, our holdings for the court at Staunton, VA at this time are quite limited. The records you are seeking would normally be named Sequestration Case Files and do exist for a number of confederate courts, but not the Staunton court. The 2 series we do have are:
Miscellaneous Records - Miscellaneous papers of the Confederate District Court resulting from trials of Confederate soldiers for desertion, appointments of Justices of the Peace, writs of Habeas Corpus, and other proceedings.
Witness Book - The entries in this volume concerning the Confederate States District Court at Staunton were entered for the May Court 1864. The entire volume, which included the U.S. District Court starting in 1827, is organized by term, listing the cases heard, names of the witnesses appearing in each case, number of days spent in court, the miles traveled to and from court, and the amount paid to the witnesses for travel.
If you would like us to search either series, please email us as Rachel instructed.
The National Archives at Philadelphia
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If you haven't had any luck in Philadelphia, you might want to try leaning on local resources. Augusta County, the county in which the independent city of Staunton is located, has a historical society and may have records (indexed newspapers, accounts, local lore) available.
Even if Philadelphia has what you seek it would be worth trying.
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This is obviously a lot of information to mull over, but given how Staunton changed hands several times during Union and Confederate campaigns during the Civil War, these land seizure records could have ended up in a number of different possible places, all of which are worth considering. While these are Confederate seizure records, which may have resulted in them coming into the possession of the Federal government and eventually NARA, it's possible that cases such as this were also adjudicated at the state or local level through what are called chancery courts.
While I would follow through on the leads above in Philadelphia and local Staunton records through Augusta County, I would also check with the Library of Virginia, whose Virginia Memory records include the most complete collection of chancery records in existence for the state. It's possible your ancestor's case records were indexed and digitized there. See Virginia Memory: Chancery Records Index for more information.
Hoping this assists you with your search.