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I see in the MediaInfo log: MultiView_Layout : Both Eyes laced in one block (left eye first). It's probably the frame sequential 3D format (FS for short). Unfortunately, it's a format that can be created by BD3D2MK3D, but not opened. There is little sense in converting a 3D movie to FS, then again from FS to SBS. It's two time a lossy conversion.
Your FS version is big: 36.9 GB ! That means that the quality of the video is probably high, but it is difficult to convert it again, as FS is a final 3D format to be played with some specific players (mainly projectors), not a format intended to be converted.
Anyway, BD3D2MK3D cannot help. I suggest to convert your movie from the original BD directly to SBS with BD3D2MK3D. You can use MakeMKV to create a AVC+MVC 3D MKV that you will probably be unable to play, but that can be opened by BD3D2MK3D.
It is theoretically also possible to convert your MKV to SBS, but that require a good knowledge of the Avisynth scripting, and you will need also a few other programs. Honestly, I can't explain how to do it without your MKV file.
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