I'm posting this as I am GMing season 5 scenarios at Gen Con. If nobody is of that faction anymore, because it doesn't exist, does anybody get that faction boon anymore?
Honestly, I'd imagine so. It'll make things easier when running season five scenarios outside of season five. No "Here, read this letter from three years ago and try to figure out your faction mission."
Although it'll make things interesting when running scenarios that are somewhat dependent on you having acquired specific items on your character that are faction based.