Your party is locked by the beginning of Chapter 2, and you are in Chapter 3. You pretty much have to kill them in the Arena. You'll see their spirits again on the Lady Vengeance, and they won't be hostile. Not having Lohse in your party will affect the Doctor quest in Act 4, and a Lohse side quest to make the fight easier will not be available
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divinity original sin 2 can you kill everyone