Normaly the link must updated (Link Panel) automatically.
If not click on the "Update Link Button". If this does not work (I experience here sometimes problems on Windows) close the document and open it again. This should show you a message that some links are out of date and you can update them.
In the Object Layers Override dialog for each instance have you got it set to preseerve the current layer visibility on relink?
That should work UNLESS you change the number, naming or ordering of layers when you edit. If you do that ID no longer knows whaat to do and always uses the current layer visibility in the saved file.