Closing as won't fix. This is a known issue, but is impossible to completely resolve: you can use expressions to refer to layer names like "Layer" & index, where 'index' is only known at runtime. Therefore if you renamed Layer1 to SomethingElse1, it's impossible for the editor to know to update the reference to it. We could fix the cases where it updates the layer name if it's constant, but the dynamic names problem remains, so there will still be cases where it's broken.
I think a better solution would be a new feature to find all references to a layer, so you can review events that use it before renaming.