ZeldaTheSwordsman

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The thing here is that if you were using KSE you should have taken note of every change you were making.

Thing is, the only actual change I've made with KSE was inserting your Ebon Hawk Armband into my inventory. That's it. All I used KSE to do here was look at the save file under the hood to try diagnosing the problem. With no luck.

Some testing and discussion with TamerBill has revealed that the "Hit Points" and "Force Points" values seen in KSE are misleadingly named. They don't store current HP and FP, but rather how many HP and FP you've accumulated from subsequent hit dice and Force dice (and they only store the pure dice total, not any bonuses from Ability Scores or feats); this is why they show as zero for a level 1 character.

So, that's a red herring for whatever's going on with Atton.

UPDATE:

I at least have something of an answer now. For whatever reason, at least with my current cocktail of mods, making Atton a Jedi before dealing with the Red Eclipse infestation seems to bug and break his ability to use the Force. I wound up having to reload a save from before I set foot in the Refugee sector after discovering that the "Intergalactic Reunification" quest is still bugged, so I decided to experiment.
I tried holding off on the conversation to make Atton a Jedi until after the Red Eclipse situation had been taken care of to see if it would make a difference.

And it did.

Why that's the case, I don't know. Could be mod issues, could be a vanilla bug (would not surprise me in the slightest). But at least I found a workaround.

That's good then, yeah the classes can cause some funny things to happen.

As can messing around with KSE, since we don't know how the back-end works it is often left down to trial and error to figure out what caused the problem and then from there it's possible to speculate as to why the back-end might result in such a thing.

This is also part of the reason I avoid KSE personally as I find it much easier to dump stuff into a container and go from there, however it definitely doesn't offer you as much freedom as KSE.