Audio Music Apps Folder Confusion

I realize that the Audio Music Apps folder and the User library > Application Support > Logic folders are supposed to be hard linked together, basically pointing to the same folder. but on my installation they are not. Although a couple of the folders are linked within these two folders, for example the Key Commands folder as well as one other folder are linked. But every other folder within these two folders are no longer linked. I have tested this repeatedly.

How on earth would I go about relinking these two folders? Or does it even matter? I'm getting the feeling that Audio Music Apps folder is the significant folder and User library > Application Support > Logic folder is only there for sake of Logic Pro 9.

Is this the case? And if not, what should I do about this?

Please advise. Much appreciated.

Corey