This was found by Randy:
I have found after looking into reconciled layers that we can turn off the notification that we all love every time that we plot by using the command
LAYEREVAL and change the variable from 1 to 0. If new layers are added to your x-ref, they still will be added to your layer properties manager "unreconciled layers" filter, but you will not have to battle that message. It is still beneficial to know when new layers are added and you can still review your new layers and reconcile them accordingly.
This command works on a drawing by drawing basis. So, you will need to change this variable for each drawing. I will change it in the template, that way with any new drawing we shouldn't have to deal with this "annoyance" anymore.