That scene was only missing in the individual two-episode volumes. It was restored for the box sets, as was the missing music during The Doomsday Machine. There are no missing scenes in the DVDs. There are plenty of music and sound effects changes, though. Save your tape of The Menagerie if you don't want to live with Doomsday Machine background music and music from the Fred Steiner LP supstituting for original scoring in part 2. The Blu-Ray fixes that with the mono broadcast track, but all the DVDs and 7.1 stereo tracks have the screwed with music.