I'm not sure I can provide very much information. What Robert says about the New England Chauncey's is correct. Nathaniel and Abigail Olcott Chauncey did have a son John (born May 20, 1798). John married Amelia Butler Goodrich on January 2, 1823, and John and Amelia had 8 sons and daughters [the last of whom was Henry Nathaniel Chauncey (b April 12, 1840) at least so far as I know]. John and Amelia did have a son William Goodrich Chauncey (b June 27, 1836). Could your William A. Chauncey have been another son of John and Amelia--maybe, but it seems unlikely. [John died in Gates, NY, and there's no reason to suppose he and Amelia moved to Harper's Ferry around 1840.]
My guess is that your William A. Chauncey was part of the Maryland Chauncey's--a branch of the family that has yet to be tied to the New England and English parts of the family. My reasons for this guess are as follows: In your message you mention William A's cousin in DC: John Simpson Chauncey who married Emilie and had daughters Lillie and Ida. Also mentioned were Minnie, William A's daughter, who married a Dr. William Fowler; and Emy Chauncey, another cousin of Wm A,who married a Thomas Harper. In your message you also mentioned a Lydia Chauncey who married a Charles F. Holbrook. These names all appear in the pension records of a John Thomas Chancey (b Nov 16 1830 in Charles County, Maryland; d in Washington DC on January 24 1914). John Thomas Chancey married Emily Jane Keane in DC on July 26 1855 (minister = John C. Smith). Emily Jane had been born in Cambridge, Maryland, on October 31 1837.
John T. Chancey was a 2nd Lieutenant in the Metropolitan Rifles, 5th Battalion of the District of Columbia Militia during the Civil War. This service allowed him to claim a federal pension, which he did. His pension file contains a great deal of information. Notably: the doctor who signed his death certicate was "W.C. Fowler, MD". "Emma A. Harper" was a witness to the widows' pension application of Emily Jane Keene Chancey (John T's widow). "Lillian E. Chancey" is listed as a daughter of Emily and John T. Chancey on this widow's pension application. "Charles F. Holbrook" and "Thomas H. Harper" signed an affidavit on behalf of John T. Chancey's original pension application in 1893. All these names seem more than a coincidence and I'd think that John Thomas Chancey was your John Simpson Chauncey. Your William A. Chauncey married Miss Prather of Prince Georges County, Maryland, as you relate. That she was from Maryland and that John Thomas Chancey/Chauncey was from Maryland leads me to suppose that William A. Chauncey's family were Marylanders.
There was a prosperous Chauncey family in Maryland by 1717. George Chauncey (died 1717) had a son George (born 1708), who in turn had a son George (b 1738). This last George had sons William (b 1775) and George (b 1768). George (b 1768) married a Frances Rebecca Dorsey on November 17 1796. My notes show that George and Frances had 8 children: John Dorsey (b 1801), William Godwin (b 1806), Theordore Edward (b 1813), Sarah Martha (b 1815), Mary Leitle, Ann Elizabeth (b 1811), James Maxwell (b 1808), and George (1798-1801). Maybe your William A. Chauncey is connected with these Chauncey's of Harford County, Maryland? [These Chauncey's also had close relatives in Ann Arundel County, Maryland.]
Finally: I'd guess your grandmother's notes were investigations by her rather than certain information, especially since she was uncertain of William A's birth year.
But, that's just my guess. I hope this information is useful.
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