The book is clearly wrong on the first two generations of Francises, as it is in several later lines as well.
My opinion has been that Francis #1 and his wife Anna had 4 children, all sons -- Eli b. 1689/m. bef. 1708, Stephen b. 1695/m.1721, Francis b. 1697/m. 1717/18, & John b. 1699/m.1737.
John could be the son of Francis #2 only if his 1699 birthdate is wrong, and the others only if both the birth dates and marriage dates are wrong.
The second Francis, in my opinion, married Hannah Bailey (b.1698), and they were almost certainly the parents of Mary (b.1729), Elizabeth (b.1729), & Jeremiah (b. 1736/37), given those dates.
William, Samuel, & Amy also seem to belong with Francis #2, given the dates of their children's births in the 1760s.
That leaves Anna and/or Hannah up for grabs -- if they were indeed two different people, it seems Anna should belong with mother Anna (& thus Francis I), and Hannah with mother Hannah (& thus Francis II).
Sarah and Susannah are also up for grabs -- I have them with Francis II because that is the way I found them in tertiary records, and I have no marriage facts for them.
Going back to Eli, b. 1689 -- he is said to have died during the Queen Ann's War in 1710, off Nova Scotia. If that is true, his three children were all born before 1710.My problem here has always been that the "book" claims Eli's son Oliver to have married in 1765 at the age of at least 55, with children born as late as 1785, when Oliver was at least 75.Either Eli did not die in 1710, or there is a missing generation, or we have another Eli -- this is typical of the book's errors.
In fact, I think the book makes a habit of confusing like names.I think it has several of the early Elis, at least two of the early Josephs, and obviously both Frances mixed up.