If you want to cut the video at a precise frame, you should add the frame number (followed by upper case i) in the "chapters_3D.qpfile" file before launching _ENCODE.cmd. Otherwise, you will only be able to cut at the next i-frame in the file, and the precision will only be something like 1 second or two. (By default, the chapters_3D.qpfile forces an i-frame at the beginning of each chapter, so if you want to cut at a chapter point, you don't need to edit it.)
Cutting with MkvMerge is easy. Look in the "global" options.
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