If it was me, I would leave it in your system. Sure, show in that one that CA is already underway to being implemented, but if this from a 2nd customer audit/issue, you can't just toss it aside; the customer is going to want you to answer it in some way, if they're like our customers.
I would simply copy your documentation of the CA and its implementation into your response to the 2nd NC.
All that said, that answer was from the perspective of "we had an issue that got us an NC, and another customer got the same thing around the same time, so we had a 2nd NC from the same issue". If you had an NC, implemented your CA, and THEN got another NC from a customer AFTER implementation, over the same problem, your CA was either incomplete, corrected nothing, or you did not dig deep enough for the real, underlying issues that would have allowed more effective CA on THAT issue.
I've been through both problems; document both NC's AND all CA.