Upgrading to Unity 2019 removes Udonsharp behaviours from the prefab objects in the scene.
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VoHeLi
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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Tupper - VRChat Head of Community
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Phasedragon
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The latest SDK (VRCSDK3-WORLD-2021.08.11.15.16_Public) will no longer delete serialized data from an udonbehaviour if it's program source is missing. We know that this does not entirely fix the issue, but it does ensure that your data is recoverable if you do run into it. Various editor scripts, including those built into udonsharp, should be able to automatically repair your project with greater success now.
100の人
If your project was created with Unity 2018.4, you can fix it with EsnyaUnityTools.
However, sharing the project with git will force the Program Source to be dereferenced. This is true not only for the prefab itself, but also when you overwrite the Program Source property of prefab instances on the scene.
This happens in both UdonGraph and UdonSharp.
In the current VRChat SDK3, prefabs including Udon Behaviour are completely unusable.
100の人
If you install the latest version of UdonSharp (the second one in v0.20.2), it seems to fix the prefab side including UdonSharp when you open a scene (including UdonGraph are not fixed).