The post by Morris pretty well sums up the status of our knowledge.
Certainly the tale of seduction found by Scarborough, White, Talley and others doesn't appear in any of the minstrel routines that I have found so far.

I don't know where he published it or if it is in his papers at Fisk, but Talley "details a bizarre tale of a well-known pre-Civil War plantation musician, Cotton Eyed Joe, who plays a fiddle made from the coffin of his dead son" ("Negro Folk Rhymes," 1922 (1949), p. 27-28).
If anyone has the original reference, I would like to hear more of it.