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In this setup, if I switch from scene A to scene B using LoadScene and if scene A doesn't have an EventSystem while scene B has one, I get "There are 2 event systems in the scene. Please ensure there is always exactly one event system in the scene" warning spam in the Console on Unity 2021.3.41f1.
This warning is logged in both EventSystem.Update and EventSystem.OnEnable (if UIElements Module is enabled). So Unity makes it very hard to avoid both this warning and the edge case you're having. OnEnable is called as soon as a scene is loaded so we must have the EventSystem disabled before the scene is loaded to avoid the warning in OnEnable. That was my motivation for calling DeactivateEventSystem in OnSceneUnloaded.
I don't know how to resolve this issue perfectly.
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Embedded event system is deactivate in the case below: