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According to Unity technician, from Unity 5.6 onward, a common practice of constructing particle system is deemed sub-optimal. It is by assigning a sub emitter to more than 1 "master" emitter, and not parenting the sub emitter under its master emitter. The requirement existed before 5.6 but was not enforced. The reason is for allowing multi-threading processing of sub emitters.

If you persist, in 5.6.0f2 and previous beta builds, the practice will trigger assertion error and crash Unity editor easily. In 5.6.0f3 onward, while playing the scene, you will be given the error message: "Sub-emitters must be children of the system that spawns them."

To fix that, you need to duplicate the sub emitter per each master emitter. Then assign the new sub emitter to the master emitter one by one.

Even though it will not trigger any more error message, for safety's sake, parent the linked emitters correctly. You may need to re-adjust the rotation after parenting.

We have asked in the official Unity forum if it is possible to handle the previous practice correctly in engine instead of requiring to manually duplicate and reassign the sub emitter. Just do not expect it to happen before Unity 2017.

https://forum.unity3d.com/threads/parenting-of-particle-sub-emitter-in-5-6.462180/#post-3026427