Wow, they have to have some idea. If they do not know, then they do not know their business and are in more trouble than everyone thinks. Granted, they have to work out the timing for the response, possible reinspection, and resubmission, etc.
You are suggesting this is the first time they heard about this manufacturing issue/concern. If it was discovered during the inspection phase of the process, then they knew about it.
What would it mean if they knew about it but thought it was a minor issue that would not result in a CRL? Sort of like if an inspector came by your house and said you have a leaky roof, you should get that fixed -- and while you are interviewing contractors, a "condemned" sign appears on your front door?