I think the complaint is that you define a resource in some module, then do a bunch of refactoring with the result that the very same resource is now defined in another module, terraform will need to be explicitly told that it's still the same resource or else it will destroy and recreate it on application.

That is, it's about the file system layout of the .tf tree, not the state.

There's also tf import and tf delete to manually import resources to your state and remove them respectively.