Possibly the question was laid to rest long ago, at least in the minds of specialists.

In a lengthy article in "American Folklore: An Encyclopedia" (J.Brunvand, ed., 1996), blues scholar David Evans writes:

"Blues first came to public notice around the beginning of the 20th century. The precise time and place cannot be identified. ...Blues was especially popular in ...the Mississippi Delta, Louisiana's Caddo Lake, and south Florida. ..."

While citing Lomax in his bibliography, nowhere does Evans assert that the Delta exclusively was the "land where the blues began."

It seems to me that roughly simultaneous popularity in New Orleans, southern Indiana, Memphis, and South Florida around 1910 would suggest many years of unnoticed development.

Presumably the intentional use of "blue notes" began ad lib, possibly to suggest a vocal moan. It would have taken a long time for that practice to become standardized into a new musical genre over a wide area.

It's been a long time since I listened to this album, recorded as late as 1974 to 1997, but I don't recall hearing anything bluesy - possibly because the banjo repertoire didn't lend itself well to blue notes:

http://www.folkways.si.edu/black-banjo-songsters-of-north-carolina-and-virginia/african-american-music-old-time/album/smithsonia

At any rate, while there's no suggestion that I'm aware of that the "blues" existed or spread during, say, the Civil War. But there's no way to know about the use of occasional "blue notes" during the 19t century. They would have gone unmentioned in print and would have originally been thought of as simply off-key.