You could say that the certified body has audited a sample of the whole of your QMS, not just the internal audit process. A large, multi-national pharma that I know, used to use the fact that a certified body or a division/corporate audit had recently performed an inspection, so any scheduled internal audits that had not been performed, such as the internal audit process, were said to be covered by the certified body/division/corporate audit.
OR. Get your management or a trained auditor from another department to audit the audit process, as long as they are independent.