Magic may well have been real. Healing crystals, shamanry, witchcraft, voodoo, things of this nature may have been real at one point and have since been patched out. These could have simply been glitches in the program.
We’ve all heard of glitches in games that can be exploited that eventually get patched. Could have been real.
Or, just phases in the game. Like, Civilization, only magic fades away when you enter the industrial age. Sure, you’ve got all this written media talking about the supernatural and magic, but there’s no enduring proof, and later generations just accept it as superstition, despite the global written anecdotal evidence.
Love it.