Yeah, so it seems somehow your appearance was permanently changed to that of a Sith soldier. That means there's nothing you could do via regular gameplay to correct it.
I can think of two possibilities. One, there's some sort of bug in the save/load system and the game eventually forgets what your appearance is meant to be. Considering you were never meant to have a disguise item for very long in the game, it wouldn't be surprising that such a bug would go unnoticed. If it is that, though, we can't fix it, so it's not satisfying to think about that.
The other possibility is some specific scripted event in the game that bugs out. My guess would be something to do with the Leviathan capture - the theft of your inventory, or switching control to a party member, or the spacesuit walk, lots of possibilities there - or module transitions, maybe the rapid transit system. If it is something like this, then it should be possible to fix, but I imagine it would take a lot of testing to nail down exactly when the bug occurs... assuming of course it isn't a random save/load error.