Does that apply to soul eater as well?
Yes, any mod. I believe eaten souls are always tied to a specific instance of soul eater, so this would mean stealing a new instance of soul eater would remove all souls you ate with the previous one, but I don't have time to specifically test that and it's been a while since I had to code anything related to soul eater, so my memory may not be completely accurate on that interaction.
Effectively each instance of Soul Eater has a separate soul stomach, and souls can only be put in one of them.