This item is provided in Fleming, 1971:364, citing a letter from Mrs. Laura Cowan Blaine, of Springfield MO, to J. Max Cowan then of Bloomington, IN, dated December 7, 1916. Fleming believes the John Cowan identified in the letter refers to Major John Cowan, son of Samuel. This is easily shown not to be the case (see below), but the story told in Mrs. Blaine's letter does bear some resemblance to the Mary Walker Cowan and Ann Walker Cowan stories.
Fleming comments at this point about Mrs. Blaine's father "his recollection of the name of his grandfather obviously was correct. he was Major John Cowan, son of Samuel Cowan, the immigrant."
The similarities between Mrs. Blaine's account and the stories of Mary Walker Cowan and Ann Walker Cowan, make it relatively easy to see why Fleming would conclude that her Great Grandfather was Major John Cowan who supposedly married Mary Walker. (Fleming seems to error here in that if Mrs. Blaine did descend from Major John Cowan, husband of Mary, he would have been her Great Great Grandfather.) On the otherhand, it is also difficult to see how this could be true. Whatever you think of the Mary Walker and Ann Walker stories themselves, there's little doubt that they took place in SW VA and/or East TN. Yet the John Walker of this story, supposedly Major John's son, is born in Rockbridge County, and marries in Rockbridge County. Not only does Mrs. Blaine place his first marriage in Rockbridge, but there appears to be a primary record, cited by Morton, 1973, that shows John Cowan marrying Margaret Weir in Rockbridge county in 1796. While this doesn't completely rule out the possibility of Major John being the ancestor of this line, it seems unlikely that his son would have gone to Rockbridge after the death of his father.
It is also worth noting that JB Cowan does identify a John, son of Major John and Mary Walker, and does have him as moving eventually to Indiana. This seems to be the same person as referenced by Mrs. Blaine (though she seems to have skipped a generation). It is possible that JB and the family of Mrs. Blaine were in communication with each other, and shared their information. Whether they in fact shared a common ancestor is another matter.
Some additional family data: Laura Blaine is shown as the daughter of John M. Cowan, in the 1910 census for Springfield, MO. She is shown as 58 years of age, born in Indiana, and widowed. John M. is shown as 88 years of age, born in VA, his parents born in VA and KY. (See Ancestry Image) This is consistent with her statement that her grandfather was born in Rockbridge.