Kamdan wrote:
I wonder if that original black and white 16mm version of the pilot included the deleted scenes as well.
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No, the deleted scenes were still deleted. The black and white print was of the final cut, so those two extra lines are the only dialogue that doesn't appear in either of the reconstructions.
(As the notes to the video indicate, an additional sentence from Pike was somehow left out of the all-color reconstruction although it was still present in the part-color reconstruction and indeed in "The Menagerie" itself.)