I think the correct way to do this is to create the two pupil spheres AS SEPARATE OBJECTS of their own, i.e. please don’t duplicate one to make the other! and definitely don’t add them in the edit mode of the traveler!
Put them in position. Then select both, and the traveler mesh, IN THAT ORDER, so the traveler is the active object, and then pick JOIN from the object menu. Now the pupil meshes will be part of every shapekey that ‘Traveler’ has, and you can edit each shapekey to make them expand or contract for example without having them disappear.
Just delete the extra shapekey ‘Happybrow 1?’ with the spheres that you created earlier in this thread, or better still go back to a version of this file before you created that. That was a mistake that may work but not the right way to go about doing it, as Eppo said not a good idea to add geometry to a shapekey. Every shapekey has to have a location for every vertex, and doing it in any way other than I have just described causes problems.