I didn't find that removing the bottom bar options helped, I called them the "Don't screw with my hotbars" settings. I turned off everything, and the game kept replacing "missing" spells upon loading.
Only fix I figured out, was moving things to unused bars, instead of just "Removing" them.
I had the exact same problem. Yet another frustrating bug in a AAA title that was released at full price. But don't worry, it's "Early Access," so the 10,000 inexcusable and embarrassing problems with the game are completely justified and normal. Because that's how the future of quality gaming works now.
