Hello and sorry for the late reply.
Is by any chance your graph an “Asset Reference” rather than a “Bound Graph”?
If you graph is an “Asset Reference”, then this is normal to happen, since by “Unity standards”, assets (that live in the Project), can’t hold references to scene object (that live in the Scene Hierarchy).
The simplest solution around this, would be to use and make the graph a “Bound Graph”. This will bind the graph with the gameobject (which lives in the scene) and thus possible to hold other scene object references.
Another solution to this if you definetely want to use Asset Graphs, would be to use “Blackboard Variables” instead of direct assigned object refenreces. Because the “Blackboard” is a components attached on the gameobject in the scene, it CAN hold other scene object references as normal.
Let me know if that works for you and whether or not this is indeed a case of using Asset Graph References.
Thanks!
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