Generalist Upgrade Decks 1 and 2 will contain the upgrades under' Genral Faction Upgrades' in each book, from the Core Rulebook through to Ripples of Fate.
The Upgrades for each specific master and henchman (if they have one) are in thier masters crew boxes and really, you won't be able to use them without those models anyway.
So if you've got, as you say, The Kin, and there's upgrades showing that you don't have in Crewfaux, they will be in the Generalist Upgrade decks.