It should be possible to convert mk3d to mkv, i.e. Matroska MKV 3D files (.mk3d) to normal Matroska MKVs (.mkv) with dedicated Matroska software like MKVtoolnix or similar.
What mk3d to mkv conversion will, is that it makes 'normal' Matroska video from a special 3D variant, possibly changing some files internally within the Matroska package. This is why just renaming mk3d to mkv won't work.
Updated: March 22, 2017