So we’ve been having this issue ever since we started using light linking in our scenes. We tried to fix it with the new render setup that Maya 2016.5 has, but nobody knows how to use it and it seems really super buggy and unfinished so that caused way more issues than it solved. Legacy render layers were similarly unsuccessful even though that had always worked fine in the past. So we’re back to rendering everything on the same layer, which means that we had to face this issue to move forward.
When using particle instancers, they completely ignore the light linking that we setup for reasons no one truely understands. However, I have figured out how to fix it.
Basically you have to grab the lights that are not supposed to be affecting the instances and multiply them by zero.
Step 1: Select a light that you don’t want to affect your instances. Create a PxrIntMultLightFilter.
Step 2: On your PxrIntMultLightFilter, in the attribute editor, set the intensity to zero to cancel out the unwanted lights.
Step 3: The PxrIntMultLightFilter can be linked to objects the same way regular lights can be. Deselect everything except the misbehaving instances and the shading groups.
Step 4: Apply the PxrIntMultLightFilter to your unwanted lights. This will only affect the instances since we linked them to the filter in step 3. Click on the unwanted light, go down to Light Filters in the attribute editor, and right click on the box to select the filter we created in step 1. Existing filters will show up at the bottom. Do this for all unwanted lights.
Step 5: Render!