Both lithium -> dilithium and lasers -> phasers were done early in the run by the people who were making the show. It was part of the evolution that any such show undergoes. TOS is a finished work and has been for over 40 years. Accept it for what it was. Trying to "fix" things just seems unnecessary. It ain't broken. It is what it is. Like I said before, should we now CGI the faces of the crew from the last movie over Shatner, Nimoy, etc? Should the uniforms be CGI'ed with the little delta pattern? Sjould the random blinky lights on the bridge be replaced with more modern displays?
If someone wanted to creadte a new artifact that used hyponeutronium then more power to them. The books should be there to expand the universe, not change what someone perceives as an error or a flaw or what have you.