Elizabeth - In another posting to this forum in 2000 (msg 319), you refer readers to the Knowlton Genealogy at www.benetech.com. The link given in the message no longer works, but I have used another link in the same website that does work and gives the genealogy beginning with the so-called Captain William. If I understand you correctly, the first generation of this genealogy (William with sons John, Samuel, Robert, William and Thomas and daugther Mary) is no longer considered to be true. If you were tied to the original posting of this webpage, you might want to ensure that it gets updated.
Secondly, the Knowlton Genealogy, published 1897 and cited in the Abbe-Abbey Genealogy, published 1916, says (quoting from Abbe-Abbey Genealogy) "an ancient grave-stone bearing the name of William Knowlton, 1632, was discovered there [Nova Scotia] by a land-surveyor in 1839." I assume that Knowlton family experts don't seriously consider this to be evidence for a "Captain William" Knowlton. It does, after all, sound like just the kind of find that would encourage story-spinning - and if it fit in with some other speculation of the time, so much the better. Is this how you see it?