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TNG also explained that teleporters could be used to cure disease by simply not re-assembling the disease part and that major discovery was also never again explored (I've not claimed Star Trek has ever been good at consistency; I just think this issue with the transporter is one that was so prominent that it will stick out to the general new audience apparently rediscovering Star Trek because of the new movie).
Of course, it would seem that within a few years the Federation should have post-TNG technlogy in many areas since Spock apparently knows all that stuff.
Maybe at the beginning of the net movie Q can show up and say "oops, let me clean all of the inconsistencies!" and snap his finger claiming it is done and all now makes internal sense.
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