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I got the same problem and as i can remember the last thing i made is changing my scriptableobjects folder path from Menu/Update/ScriptableObjects to Menu/ScriptableObjects and all asset reference were reset to null, like image or reference on other scriptable objects. The other varibles like string, int, float etc hold their value correctly. Im working on collab i tryed to revert but by changing the folder, i lost my history so its anoying to reconfigure all my scriptable object for the third time.

I have found a ridiculous way to fix this.

if you hit play, you should be able to see the data contained in the scriptable object files.

while playing, right click on the files in the projects tab, hit reimport (yes.. while playing), if the data is not corrupted, you should have recovered the data from your missing scriptable object.

Coming across this bug report has cleared up so much ambiguity with asset database bugs my team has run into. It has gotten to the point where people close the editor before syncing on source control.

This is a huge frustration on a daily basis and leaves people just angry at the editor. Please consider reprioritizing this as it should be expected that developers pull in changes from source control regularly. The fix note seems to imply that using source control when the editor is not open is not supported. This is not a limitation that should be expected in modern software development.

For anyone stumbling upon this issue, I may have found a workaround. The references I had to a ScriptableObject would be equal to Unity's "null", but they wouldn't have a name and I couldn't get the GUID from them (which would be required to load the asset again). However, calling GetInstanceID() returned a valid instance ID. Curiously enough, this is the same instance ID as the real ScriptableObject my reference is failing to find. Calling "EditorUtility.InstanceIDToObject(id) as ScriptableObjectType" would return the reference I needed after getting the ID from the "null" reference.

I was forced to do it this way since none of the standard functions for refreshing or dirtying assets seemed to fix the null references. SerializedObject.Update(), SerializedObject.ApplyModifiedProperties(), Undo.RecordObject(), EditorUtility.SetDirty(), AssetDatabase.ImportAsset(), AssetDatabase.Refresh() and AssetDatabase.SaveAssets() do NOTHING to fix the references.

I wish Unity specified in their resolution note what they meant by "reloaded again manually" as it would be impossible to reload a null reference without getting it's path or GUID (which is impossible to get from the null reference AFAIK). You could serialize an additional GUID string for any ScriptableObject reference, but this seems like a waste when the GUID is already serialized to store the reference in the first place.

Unity will automatically fix this "null" reference issue during a recompile or when you quit the application and open it again. What is frustrating is that Unity must have some internal method for updating ScriptableObject references, but it is not made public to developers. This issue wouldn't be so bad if we could simply force Objects to update their ScriptableObject references by calling AssetDatabase.UpdateAsset() or something.

It is unfortunate that Unity has no current plans to address this, but at least a workaround exists for now. Hopefully the new "Addressable Asset System" resolves this when it releases. I would also strongly encourage Unity to put this information in their documentation, as I spent hours trying to figure out why none of the functions I mentioned were fixing the issue.