Opening a 2018.3 project in 2019.1.0b1, causes all UnityEditor.SceneAsset references to go missing. I submitted the example project with 2018.3 on purpose, to allow you to see that it works in Unity prior 2019.1.0b1. Spoiler: Screenshot Reproduce Open attached user project in Unity 2018.3 Select "Assets/TestAsset.asset" Notice in the Inspector, that "Element 0" points to "Scene" Open attached user project in Unity 2019.1.0b1 Select "Assets/TestAsset.asset" Actual "Element 0" shows "Missing (SceneAsset)". Expected References should stay intact when upgrading the project. Note The scene .meta file guid didn't change and is still in the project though.