Defictionalization: In keeping with the new British tendency to de-fictionalize literature critical of the local government (i.e. Nineteen Eighty-Four), there now really IS a N.I.C.E., and the cynical see it heading in the Police State direction. (In Real Life it stands for the National Institute of Clinical Excellence, an organisation which decides whether drugs are worth the cost for the NHS to buy or not. The unfortunately coincidental choice of acronym makes it easily demonized by American "death panel" anti-Obamacare propagandists, and people who are upset that it won't pay millions of pounds for drugs that might give end-state cancer patients a few more months of life.)
The stated goals of the Voluntary Human Extinction Movement are starting to sound quite a bit like the secret goals of N.I.C.E.
Science Marches On: The canals on Malacandra. Science had already questioned the existence of canals on Mars and Lewis was aware of this, but included the canals anyway.
Also the oceans of Perelandra, back before it was learned that the surface of Venus was a volcanic wasteland hot enough to melt lead. One of the sorns in Out of the Silent Planet actually mentions that any being from "Parelandra" would logically find Mars too cold to survive in, but Lewis clearly changed his mind to make for a better story.
What Could Have Been: The Dark Tower, a fragment story that got abandoned in favor of taking the sequels in a very different direction.