When doing regular work in 1.3b2, I got the following error:
There was only one Scene Variables component present in the scene (I ran a search), and only one scene loaded. It persisted through restarting Unity. To eliminate it, I removed the Scene Variables component, let Bolt make a new object with the Scene Variables component and copied the values of the Variables component to the new instance. Then removed the old instance. This fixed the error.
I do not know the ultimate cause, as it just appeared and I've only gotten it once.
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