The logic behind this is that the writing accounts for either Brint being the same or Brint becoming Brienne by the time you meet his family, but trying to account for 'Brint could become Brienne at any point in their associated content' would basically require writing a ridiculous number of variations to account for. Hence the game enforces that you either get Brienne before entering the KM Outskirts or you've cut off that thread forever.
Mind you, the game gives you fifty save slots built-in and as many of your own as you care to make. IF you don't want to get caught up like this in the future, consider making a few backup saves at various points so you can unwind progress. I'd also suggest checking your auto-saves but if you've played for any significant length of time past first entering KM (ie, ten hours), odds are that all your auto-saves are too new for one to still exist that's before that point.