In the Empyrean well you cannot access the top floor even though it is underneath the rim opening. When using the climbing picks to get up there you are instantly killed. Your companion can revive you, and then you are stuck in place. You can use the climbing picks to pull yourself out, but can't explore that level. When trying to figure out the puzzle, it sounds like there might be a pylon above you (on that top floor.) Also when trying to use climbing picks to grapple onto one of the floating rocks in the middle I got stuck inside one of the rocks, and had to use the "Unstuck" function to get out.
Also if you go down to the very bottom and jump in the well you are ported to the top onto a place you can stand, but still take damage from the well effect, so it is useless.