if you die and go into creative then give yourself a soul crystal then go back to the other one where you died there doesn't appear to be a way to delete it form the world not even a command or something.

I found out, while you can't teleport the soul crystals with /tp, you can still delete them with /kill. The entity ID appears to be enigmaticlegacy:permanent_item_entity. So you can, for example, use the following command:

/kill @e[type=enigmaticlegacy:permanent_item_entity,distance=0..10]

This will delete all soul crystals within a distance of 10 blocks. In my case I had to do this because a soul crystal was left behind after I deleted a player's files to get them to start fresh.