That I don't know, he is pretty tight lipped about spoilers, I am trying to give him ideas for bringing her back though.
If you kill him then she admits that she loved him and gets upset, if not, then she admits that they are going to get married.
How this will affect the later story, I can only say one thing for certain, dead men can't fight in wars.
Personally, I am hoping that after the war, we can find her, cure her, and take her in.
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As for the saves, I will take a look, but I am not a coder, so I can't do much more than check a couple of things. If I can't figure it out, I will make sure that Archon knows when I see him, if he hasn't been here first.
All 3 of you having the same issue?