Yes. And the number of the 3D-Plane associated with a particular subtitle stream is stored in the MPLS file on the 3DBD. Since that file is lost when MakeMKV muxes the tracks to the final MKV 3D, the 3D-Plane number was lost too, but I have asked to copy it in a special tag. That information is therefore available now (and is used by BD3D2MK3D) when the 3D MKV has been created by MakeMKV. I don't know if it is possible to modify or specify that tag manually.
BTW, a similar problem existed for the order of the main and dependent video streams (left/right or right/left eyes). With old versions of MakeMKV, that information was also lost, then incorrect, but it should be available and correct now.
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