I had this same problem minus the megascans. In my case I wanted 4 lods 4096,2048,1024,512. I created the extra material inputs before I baked them out. I baked 2048 out from the screen where you set up lods, instead of the details in the main editor. instead of it putting it in the lod I assigned it to, it actually made a 5th lod. then I couldn’t delete any of the lods and it was greyed out. My fix was way more simple, I just reimported the model when I went into the screen UI to set up lods, x was now lit up and I could then delete them. hope this helps