The issue happened for me with Udonsharp while I wanted to upgrade my project to Unity 2019. I have tried multiple times and followed the migration instructions and after reimporting the sdk at the end, all my udonbehaviours which have prefabs got unlinked as it is shown below. The behaviour prefab itself is still working as well non-prefabed objects, but the instanciated prefab in the scene got all its data removed.
I would not like to fix it by hand for me since I have hundreds of UdonBehaviours in my scene.

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