This was stated by several people here in the forum. I think you guys are really (extremely) really lucky to get these characters back! It was totally clear that you would (normally) never ever be able to get them again! Or the other way round: As soon as it was clear to the devs, that some character specific missions would be implemented in the future, they should have "blocked" these specific characters from sacrifice. Or communicate on that in some way. Well I think the lesson might be learned for both sides.
My general advice: never sacrifice a non-dupe or accept the risk as we know (now) that missions change, character tuning takes place...