_ENCODE_2D.cmd is the command that launches x264 (or x265) with the required parameters to encode the movie in 2D, in case you are interested in the 2D version alone. If I have correctly understood your choice, you don't need it, since you encode in full-SBS so that you can select only an half of the video image to watch the SBS movie in 2D. But others (including me) need half-SBS and having the possibility to encode also in 2D is handy.
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