When a light that uses lighting channels is only visible in one view during stereoscopic rendering, it affects the default light channel instead of the assigned one in the view that it's not visible in. Happens both with and without instanced stereo enabled.
Found on //UE4/Release-4.11 CL-2944320
Alternatively, set up a map with some moveable objects set to lighting channel 2 only, with a spot light set to lighting channel 2 only as well. Then move the headset left to right across the objects, so that one eye cannot see the objects or light.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-29513 in the post.