A lot has happened since then. Building on information supplied by descendants of Margaret Hughes Van Cooten I have been able to extend the family tree for her descendants.
The advent of DNA testing has introduced the ability to match the genetic tree with the genealogical tree. In this case, there are good matches between John Hughes Van Cooten’s descendants and those of Margaret Hughes. This confirms that they are siblings. A match with a descendant of John and Margaret’s half-brother John Rhodolphus Van Cooten confirms their relationship as being descendants of John Lucius Van Cooten.
I’ve yet to identify a match with descendants of Emma through her first husband Henry William Hewes.