Effects of using black separation crystal?
These are the uses of the stone (Informative to those who doesn't know):
Sends back phantoms in your world (not invaders) to their world.
You being the phantom, this stone sends you back to your world (Also works if you're an invader).
Vanishes NPC phantom allies (beware as their summon sign won't appear again even after resting at the bonfire. A friend of mine mentioned that it shows up again if you reload the game.
If you're the host and use it, you can see your victories as a phantom.
Actual Answer
The reason for the "beware fickle use of this item" warning is because if you use it either as a phantom or as a host to send back people, you are committing a sin. I've only tested it as the host sending someone back and it did add me sin.