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I don't use MakeMkv, but I think that it can do a backup suitable for BD3D2MK3D. I think also that you can back up the main movie only, and that's of course an advantage in term of disc space.
You need an ISO or BD files in a directory on HDD for BD3D2MK3D. BD3D2MK3D can't accept a MKV as input.
Sorry, but I can't tell you more. Perhaps someone else can confirm?
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