I knocked her out but she never appeared at moonrise.
You have to knock her out while she's "temporarily hostile" in the goblin area. Once she's at the raid on the grove it's too late.
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I find the idea of Minthara fleeing combat to be a more elegant solution to finding her later at Moonrise.
The idea that she doesn't retreat because she knows what will happen to her at Moonrise doesn't make any sense to me. For some reason, she goes back to Moonrise after being knocked out, but won[t retreat? At some point we're just throwing wild interpretations against the wall regardless of inconsistencies.
If the goal is to allow Minthara to be at Moonrise even if the player didn't ally with her, then the method of doing so should make as much sense as possible. Her retreating from a lost cause makes more sense than just randomly bonking her on the head and knocking her unconscious, which is oddly one of the only times a player probably knocks an enemy unconscious instead of dealing a death blow.