TServo2049 said:

Actually, I believe what was located was color silent negative just for the stuff that was cut out for The Menagerie. A couple scenes that were used in The Menagerie had extra lines of dialogue on Roddenberry's print that didn't show up in any of the official releases, so I am assuming they were missing from the negative. (Not sure why they weren't in the hybrid version either; regardless, the only way you can hear these scenes are audio recordings from a sci-fi convention that are on YouTube.)

There was apparently a color print of The Cage, in private hands, that had completely faded to red. It was on eBay once, but I believe the reserve was not met, and now it seems to have been chopped up into individual frames to be sold as collectibles (not by CBS/Paramount, to be absolutely clear). I guess we will never know if it had the missing stuff that was only in the B&W 16mm.

That is true. The negative was cut to use certain scenes for The Menagerie and the rest was put away. This is the negative that was later discovered for the restoration.

Interesting about the lines. I looked them up on Youtube. It's not very much, but it bizarre why they would be missing from both the restored versions...? It could be that the first restoration had some missing frames and cut around it and the new color restoration used the previous "edited" restoration as a guide.