I’ve accidentally found out that if you rename inputs in a base metasound, then any presets that had that input exposed and overridden will default. In the case of a wave array, if you had assets in the wave array, they will default to not being overridden and therefore empty (since we keep wave arrays empty in the parent metasound).
I was very surprised by this. Is this a bug or feature? Seems as though it makes it quite difficult to make changes to any inputs that are already being used by presets.