When converting an embedded graph to a macro, the graph will loose all scene object references that were previously embedded into that graph.This probably is expected but UX is bad, resulting in mistakes that can't be easily undone. E.g. at first, nothing seems wrong with the graph because after conversion, the object references can still be seen as valid when looking at it in the graph view. But after going into play mode or reloading the scene, the references are gone. The conversion process does not inform about the potential loss of information.
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