In fact, almost everything is already in the Project directory, as thahandy has discovered. The necessary files are already demuxed, and there is already a file to mux the 2D MKV. The only thing that is missing is the command to re-encode the 2D video, and a modified MUX_OPTIONS file to mux it to MKV.
I think I'll do it later, but currently I haven't much time, because I'm helping slavanap to debug his work. It's something much more important and valuable for us, including (indirectly) for BD3D2MK3D. I'll let you know when that will be ready...
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