Audit? Auditors don't have access to the BSA data base; they cannot obtain baseline information for comparison to your file copies. Examiners do. I referred to an examiner as an auditor once. It was a few decades ago, but I still remember the tone of voice he used when he corrected me.
If CTRs were not received in Detroit, examiners generally take the perspective that they were not filed. Sending paper CTRs return receipt requested doesn't prove what you need to prove. I've seen examiners just shrug and say, "The receipt proves you mailed them an envelope and they got it. It does not prove what was in the envelope." My experience is they will cite you for not filing the CTRs.
Given the ridiculous way paper CTRs are handled; i.e. from Detroit they are sent to an Indian reservation in the Dakotas for input, it's amazing that more of them don't go amissing.
Here is a pdf copy
of the ppt slides from the FinCEN webinar on the benefits of e-filing. One of those benefits is that you automatically have proof of filing.
It's time for the hold outs to just sign up... Problems like this are just a waste of everyone's time.