At the time they were pushing this story, some honest historians opined that it was Jefferson’s unmarried nephew who fathered the children. I don’t know what this might say about Thomas Jefferson himself, to allow this to go on, but at least that was one view of the situation. I also do not know the chronology relative to his wife’s death, Jefferson’s hitch as Ambassador to France, and all his other duties all over the place.
DNA ruled out the Carr nephews.