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Unity3D Script loses serialized data after .dll update.

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I have a custom editor which saves its data in a Monobehavior attached to the object its editing. This data saves fine and persists between sessions/play mode, etc. Both of these classes are included in a compiled dll that I've made and included in my project. My problem arises when I update that .dll - suddenly all the serialized data in the MonoBehavior class reverts to default. This is hugely problematic because it would prevent updating the .dll in existing projects. How can I prevent this from happening?

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