This might be less of a true bug than a failed quest state?
Similar to the Defending the Outpost quest, it might be useful if there was a way to make sure the Daughter appears when triggering the Flame Prophet.
Alternatively, having your quest journal update for a record of the death so you can complete the quest once it starts (e.g. "Oh, I already killed her..." dialogue option).
There are more than enough ways to get black shards in the game (unlimited if you count hunting rumor bosses). So, you're not stuck in the game. You just don't get the option on the flame prophet's pendant, or her help with the Undermother.
Moved to Support.