Naomi was a transporter accident.
Did they reintegrate the quantum duplicate walking around with the baby corpse in the EMH's freezer at some point?
B'Elanna was a transporter accident after Faces.
Drone was a transporter malfunction and Mulcaehey would have insisted that part of his essence was stolen and that he medically needed it inserted back inside him.
NAOMI: And once, there was a transporter accident. Neelix and Commander Tuvok got combined to make a completely different person.
NAOMI: You don't think I could make up a story like that, do you?
BRAX: Hello, Neelix. Do you want to play kadis-kot?
NEELIX: Maybe later. (Dexa and Neelix move away)
From in the Flesh
CHAKOTAY: Turns out the transporter malfunctioned. My uniform ended up in the pattern buffer.
ARCHER: You're kidding. You were naked?
CHAKOTAY: Not entirely. I had my commbadge.
ARCHER: I hope it was well-placed. Computer, lights.
the Indian only suspects that his uniform was in the buffer... But what if he had metabolized it?