The idea is that Raiden "cleansing" the Jinsei chamber from Shinnok's "aura" corrupted him, similar to how his soul was tainted by Shang Tsung and Quan Chi while their souls fought after dying in MKD's intro.
But none of this was explicitly said, and even if it was, with how much NRS loves to retcon stuff and give powers to that amulet anything could happen.
