Various unskilled ponies can see Luna's exposed soul

 the lift had reached its destination: a large round platform in the very middle of the swarm of souls. The inclinator slid into a berth, and there was a series of clangs as plates locked the mechanism into place. In the center of the platform was a strange, vaguely familiar design etched in the metal floor plates: a circle with a six-pointed star in the middle. Six unicorns, one standing at each point, were trying to keep a ball of brilliant white contained in the middle. Green lightning from their horns raked across it, forcing it back whenever it drifted. The black robes they wore were a little much.

He then gestured at the bright soul being held by the straining unicorns. “THAT is a Princess.”

“What?” I gasped, sitting up a little and staring at the glow. Maybe it was having organic eyes again, or maybe it was Discord’s presence, but as I stared, I detected something within the mote. Something beautiful and wonderful and mysterious. Dark, but not the bubbling evil that had been inflicted on me before. It was glorious and terrible, and I couldn’t tear my eyes away as I beheld it.

The soul of Princess Luna.

“You’re a bit of a packrat, aren’t you, Cogwheel?” he asked with a grin, going back to petting my head as if I were a cat. “You collect things. Little bits of this and that. Ponies. Souls. Cities. A bad habit, really. One that’s going to get you in trouble.” I felt him tremble under me, but I couldn’t tear my eyes away from that soul. “However did you think you’d get away with keeping Princess Luna’s soul?”

Fallout Equestria Project Horizons Chapter 65