Like in my previous post, you can choose to not believe her/it. Honestly, I don't really believe Alt to be the most trustworthy (although she has no reason to lie) and probably not the best place to talk about this.I'm not left with impression that Soulkiller is some defective product that can't do the advertised copying job.
Equally i don't see how AI Alt can know for a fact that something like a soul which is completely intangible/unmeasurable is lost in the process.
May just be the internal logic that she is built upon.
For other characters, there is no problem with that. Like Goro, Johnny or even Saburo who intentionally used the Soulkiller on him (Proof that he thinks it is safe and that he loses nothing).