I'm pretty sure the prevailing feeling at CBS these days is that TOS isn't canon [...] i.e. Kirk and Spock wouldn't be amazed by the "theoretically possible" cloaking device in "Balance of Terror"
I'm pretty sure one line being slightly contradicted (though still easily explained away by technobabble) doesn't constitute the "erasure" from canon or any intent to do so, otherwise half of Star Trek would be "erasing" the other half constantly...