(spoiler warning)
I *think* we are both on a "good" route, but I'm not sure because I've strictly avoided spoilers. For reference, on her record, Celeste has reverted to a valkyrie; on mine she's not quite there yet (I drained a bit more early on). All characters that have ever joined the party are still alive, I think. The only named character I recall dying is that paladin you fight a couple times (I remember being somewhat surprised that he died for real after the second fight). I do not recall any duels with Malayna since the beginning.
Since we have two affected records and two non-affected records, I *might* be able to reproduce it when we reach that point again. I will try. If it doesn't happen, maybe I can diff the two save files for discrepancies. I could also try reproducing under both the current and previous versions, if the old one is still available.
If the bug only occurs with Malayna, maybe the bug doesn't involve the last fight in general, but the last fight where she was present? I don't have any evidence of that, it's just where my head would go if I were debugging it myself.
I should have an opportunity to experiment later this week, or the weekend at latest.
[edit: I remember one other odd thing that might be relevant. I've seen Malayna's "Celeste's down, now I'm pissed" vengeance line trigger sometimes even when she wasn't in the party. I didn't think much of it at the time, and it didn't seem to break anything; I mention it only because the same character is involved.]