You don't really need to know the exact specifics. That's enough.

Twilight, Bertie, and some others used a magical chalice Bertie found in Canterlot to extract my soul from my body, and then they separated the Mechakara parts from me. But without him... [This part still bothers him some.] ...well, to hear them tell it, there wasn't a whole soul left. It wouldn't go back in.

So each of them put a little bit of their soul in, to add to mine. [He sounds a little miserable about it.] I would have told them not to do that if I'd been conscious! Nobody knew what would happen.