This appears to still be happening in 4.17.2 and seems to be caused by instanced static meshes not being correctly drawn into both eyes in the depth only pass if the same material is used for multiple instance meshes. It can be fixed by changing the comparison in TDepthOnlyVS::SetInstancedEyeIndex (DepthRendering.cpp) from ‘EyeIndex > 0’ to ‘EyeIndex >= 0’.
Later edit: There are some other instances of this same bug in other shaders as well, a search for “EyeIndex > 0” will find them.