Hmm. Updating from NodeCanvas v2.6.2 to v2.8, shouldn’t have created such problems (but updating from even older version 2.6.0 should), since there was a big (and partially breaking) serialization change that took place at that time.
The error log you posted GameObject (named '@autorun') references runtime script in scene file. Fixing! denotes that there is still a leftover “non-monobehaviour” graph object attached on some gameobject named “@autorun” (since that how it used to work back then), which needs to be removed manually for the reasons you mentioned (it appears as a null attached object due to Unity serialization change as well at Unity version 5.5, while it used to work fine in Unity version before v5.5).
Does this only happens in that one particular scene?
The offending gameobject could also be a prefab, so please do check your prefabs as well for such leftovers.
The offending gameobject should normally get selected when you click the log line within the unity console.
Please let me know.
Thank you.
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