I've found your line up to Isaac also, and I keep trying to find where it intersects my lineage which goes back to Pierre Baudouin (Peter Bowdoin) who settled in Maine from La Rochelle, France (via the Huguenot colony in Ireland). All of the conventional wisdom says that all Bowdoins in the US are derived from this family line, but it seems like that's either untrue or there is a missing link.
I have a theory that your line and my line may be related in France, and from there diverged in the Huguenot mass exodus. A lot of Bowdoins settled in Quebec from Europe, and many of them migrated south to the US. So I wonder if our two lines are distant cousins who've geographically merged sometime after Pierre arrived.
One thing I've discovered in my search is that the various spellings of Bowdoin/Bowden/Boudin etc are all the same line. Baudouin sounds like the anglicized Bowdoin (bow like toe) and many of the misspellings come from phonetic interpretations from Census takers and the like. So definitely consider that alternate spellings may be related. I too want to see how Isaac connects to Pierre, and I'm thinking the clues are in Canada, then back around La Rochelle, France before 1680. I'd be interested to know if you've learned anything new since your post.