Nothing got lost.
The original versions are still available. They are also on the Blu Rays.
Are we sure about that? It's already been reported that a shot of Spock's tricorder from CotEoF has only the enhanced version. Maybe there are other shots where they inadvertantly didn't provide the original footage.
Personally, I didn't notice the above change, but I'm just pointing out that there's the possibility of original footage not being available on the blu-rays.