A licensee reports that the values of an FInstancedStruct do not get properly duplicated if they differ from the default values of the Actor or TArray to which they belong.
Possible short-term workaround:
The issue indeed seem to be the implementation of EditorUtilities::CopyActorProperties which does not copy the full struct, but just individual uproperties. Since instanced structs do not have uproperties, nothing gets copied.
Removing the bNeedsGenericCopy = false; from the struct case in the above function, will fix the issue, but I'm not sure what other issues it might bring.
Expected:
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There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-204788 in the post.