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.