In MO Union Citizens File one Francis Carney describes being arrested by Col John C Boone who then wrote out a Confederate parole near Glencoe MO. July 1863. see https://www.fold3.com/image/280265941
Further in the file is the actual parole (2 pages further on).
Boone himself has a Union Parole on file from May 1863 https://www.fold3.com/image/280258385 The signatures on the 2 paroles match.
Bruce N. has a paragraph in his venerated 1861 Guerrilla Warfare in Missouri series on him as a recruiter in St Louis and Jefferson Co in 1861. Thus it appears that John C. spent at least the first part of the war in the St. Louis area recruiting spying and making himself a nuisance. I am not sure how his father's legacy impacted his military career but I am sure it did if only by opening doors with well known Southern sympathizer figures like Sappington and Dent in the St. Louis area.
The middle name controversy comes from the question of whether Nathan Boone named his youngest son after his father's friend Judge John Coburn who helped Daniel with legal advice/petition in trying to get Missouri land returned to Daniel or John Colter a Lewis and Clark expedition vet who was a friend and neighbor of Nathan's. I've not found a definitive reference for either middle name. The fact that John C was married to Mary Wardlow first and then Nancy Bryson McQuarry 1867 Benton Arkansas, is supported by the family tree published by Draper Lyman edited by Hammon(University of Kentucky Press 1999/2012) in his interviews with Nathan Boone. Sadly I found nothing in the work other than reference to John C. Boone. Draper does report he was living in California at the time of the interviews in 1851 which would indicate John C was a 49'er with many other Missourians. He has 2 grandsons buried in the family cemetery at Ash Grove who died on the same day, which leads me to believe he was residing in SW Missouri in 1848. Mary Wardlow Boone is buried in Bellefontaine Cemetery St. Louis, Block 81 lot 1782, buried December 29, 1904. This would indicate a divorce/separation between 1858 and 1867 in the middle of which is his Civil War service. Mary Wardlow Boone has a 1904 death certificate and grave permit using her married name Boone. (Indexed under Mary C Boore)
Josie Ione Boone McGhee born 1870 to Nancy Bryson and John C Boone died 1904 in Dawes, Ottawa, Oklahoma, is buried in Williams Timberhill Cemetery, Welch, Craig County, OK, not Mcdonald County Missouri as many web reports list.
Nancy Bryson Boone death certificate is here which supports the 2nd marriage.
1850 Census USA Boone, Greene, Missouri
Home in 1850(City,County,State):
Household Members: Name Age
John C Boone 26 1824 MO Male
Martha V Boone 6 1844 MO Daughter
Mary Boone 27 1823 VA Sister
1860 Census USA St Louis Ward 9, St Louis (Independent City), Missouri
Household Members: Name Age
Jno Boone 43 1816 MO
Mary C Boone 41 1819 VA
Mathew Boone 14 1846 MO (should be Martha)
Nathaniel Boone 2 1857 MO
Mary C. Boone
Birth Date: Abt 1820
Home in 1880: Hannibal, Marion, Missouri, USA
Street: 6th St
Dwelling Number: 33
Relation to Head of House: Self (Head)
Marital Status: Married
Father's Birthplace: Virginia
Mother's Birthplace: Kentucky
Occupation: Keeps House
Neighbors: View others on page
Mary C. Boone 60
Lorance N. Boone 22
Mattie V. Bourne 32
Name: Mary C Boone
Birth Date: Dec 1826
Home in 1900: Central, St Louis, Missouri
House Number: 8
Sheet Number: 48
Number of Dwelling in Order of Visitation: 903
Family Number: 919
Relation to Head of House: Mother
Marital Status: Widowed
Nathan L Boone 41
Emily Boone 39
Hudson W Boone 7
Olive Boone 3
Seymour Boone 2
Mary C Boone 73
Olive Lorance Boone Culp related on 10/4/1960 that her grandfather John Coulter Boone was "born in the large room on the first floor of the stone house in the Femme Osage Valley".
Accomplished violinist, according to the book, "Nathan Boone the Neglected Hero", Compiled and Edited by Carole Bills.
"My Father, Daniel Boone:The Draper Interviews with Nathan Boone" By Nathan Boone, Olive Van Bibber Boone, Lyman Copeland Draper, Neal O. Hammon, 1851
Publication: Name: University Press of KY, 1999;
"Nathan Boone and the American Frontier" R. Douglas Hurt, 2000, University of Missouri Press