I found that if I try to add another instance to an InstancedMesh on a frame(?) after the one on which the InstancedMesh is created, the second instance it doesn't appear.
Updated fiddle: http://jsfiddle.net/d4oq5ahx/
If you modify instanced data, you also have to set InstancedMesh.instanceMatrix.needsUpdate to true.
Please use the forum or stackoverflow if you need more help.
Ah OK. The documentation says this..
.instanceMatrix : BufferAttribute
Represents the local transformation of all instances. For internal use only.
Yes, the documentation should be better in this case. How about:
Represents the local transformation of all instances. You have to set its needsUpdate flag to true if you modify instanced data via [page:.setMatrixAt()].
Let's give this a try.