Nothing got lost.
The original versions are still available. They are also on the Blu Rays.
Welllll, not quite. Every release of Trek on home video has had changes and alterations, both intentional and not, from the one before. There has never been a 100% accurate, unaltered release of Trek as a series on any video format.
The blu-rays have their own hiccups, mostly to do with the mono sound and goofs on the new/old effects toggle option, but don't let it fool ya - the "originals" are no longer available. Even the previews are different than the NBC run (except the 3rd season).
The only episode on the entire set which is probably exactly the same as when it was first viewed is the unaired version of Where No Man HAs Gone Before. I'm sure many folks are annyoed that it didn't get the same meticulous care as the rest of the series, but I was thrilled: no tweaked sound, no super brightening, no misplaced music - just cleaned up, unenhanced Trek. And damn, those effects look just dandy. ;-)
But, honestly, the closest thing we have to wathcing the show "as it was" is on the VHS and Laserdiscs. And I hope my LD player holds on for a while, since I have the whole series in that format. I bought it new a few years ago, during a wave of Pioneers being manufactured. Cost $1000, but it was worth it. Plays DVDs too. :-)