Regardless of the status of a character's soul in their canon (or their lack of it, in the cases of robots, etc), they will get a soul in the SC setting as a suitable and appropriate adaptation of their personality/traits. It is not necessarily the same soul that they have in their own worlds. However, it might be easiest to simplify things and say that the character's soul is transferred back to their body and adapted to the SC setting. If the item is not a weapon, you also have the option of letting her keep it, provided that its functions and uses will be removed.