I think this broke when upgrading to nested prefabs, haven’t touched the scenes since then. But now I. Hanged alot of prefabs and this message is displayed
Can i find all broken prefabs in scene?
You could probably iterate over the prefabs in your scene(s) and search for prefabs that are disconnected using the PrefabUtility.IsDisconnectedFromPrefabAsset(yourAsset) call.
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Our older scenes are completely messed up 
I guess they will have to be broken. And fix little by little. Only problem is that I cant change prefabs and these will reflect changes.