I ran into a similar challenge 30 years ago. The subject was electronic retention of adverse action notices under Reg. B, but the challenge is comparable to what your auditors may be saying about CTR filings.
My bank's credit card division (now Capital One) had a huge volume of adverse action notices, so the business unit automated the process and switched from microfilm of hard copies to electronic retention of letter segments and denial codes. The system had been used for years before we were criticized during a Fed compliance exam. The finding surprised me, but at the end of the day, I agreed with their observation that the codes we were retaining were input codes, not the processed output. There was no objection to the electronic records, only to the fact that we were not retaining copies of what was actually sent, but rather what we intended to send.
Check to be sure your records are captured from the output stream of the system that generates the CTR filings before telling the auditors to pound sand.