So, I went to a lot of effort to achieve Hero Mode ++. And to beat the game on NG+ without any generic recruits. And I did! And I got awarded both in-game achievements!
Then I went back and completed the last side quest.
Now the in-game achievements don't show me having either of those achievements.
I'm disheartened, and as I don't have a recent back-up (my last back-up was before I beat the normal game) don't have the desire to keep playing in the circumstances. I guess I'm a completionist, as I was trying to get ALL gold stars, ALL achievements, just... to do all of it. But now I have lost all of the "no generic recruits" achievements.