Okay, I've had two conflicting files that I've never had a problem working around before. I have two mods that make Atris and Darth Traya (Kreia) harder, and they both use a file called n_darthtraya001.utc. What I would do was play the game up until the part where you face Atris with the first file, and then simply remove it from my override directory and replace it with the second one after that.
Now here is what is happening: I am using Stoffe's "Handmaiden Choice for Females" mod, and everything went fine without any problems all through the cutscenes, when Brianna fights Atris and when the Exile fights her for the first time. However, once she goes off to her meditation chamber, lo and behold, there is Darth Traya (Kreia) standing in her place. I tried removing the mod and dropping it back in fresh as well as trying it without it in there at all, but Kreia is still there where Atris should be. I saved right after coming to Brianna's rescue before chasing Atris toward her meditation chamber, and I only keep one save file, so loading a game before that point is out of the question.
So how can I fix this? Will I simply have to sit through it and endure fighting a Kreia with Atris' voice?
EDIT: Oh, wait... There is the autosave, which should correct the problem. Nevertheless, I'd still like to know how to fix it on my manually-saved game.
Now here is what is happening: I am using Stoffe's "Handmaiden Choice for Females" mod, and everything went fine without any problems all through the cutscenes, when Brianna fights Atris and when the Exile fights her for the first time. However, once she goes off to her meditation chamber, lo and behold, there is Darth Traya (Kreia) standing in her place.
Without knowing what other mods you use it's hard to say why that happens, but the Handmaiden Choice mod installs a modified version of the a_kreatris script which has the player gender checks replaced to trigger the Maiden vs Atris scene if HM is present instead. This script also spawns Atris into the area in the proper place.
If any of your other mods have done any changes to this script you'll need to figure out what they have done, modify the a_kreatris.nss file that should come in the source folder of the Handmaiden Choice mod to apply those changes, recompile it and put the resulting a_kreatris.ncs file in the override folder.
(I think Achilles difficulty mod changes this script to use n_darthatris001.utc instead of n_darthtraya001.utc for example...)
As for fixing an existing savegame the easiest way is probably to make a script that destroys the current Kreia-Atris and spawns in a new Atris-Atris in her place, and then run this script in-game after the HM fight before going to visit Atris in the Holocron room.
(And playing TSL with only one save slot is like playing Russian roulette... you might get lucky, but there is a significant chance there will be unpleasant consequences. :))