Lynne,
Yes, it applies. That's why rlcarey queried the original poster for a little more context to assure he knew what was being asked. However, the thread just took off without the response; it chose its own path.
If you find an individual or mutiple CTR's that were not filed on a non exempt customer, there is no backfiling determination or the equivalent of a "waiver" mechanism; i.e. you simply file them as soon as you can. The general suggestion is that you attach a memo to your file copy explaining how the error occurred, how it was discovered and what steps were taken to assure it will not happen again.
Mistakenly failing to file a CTR might be classified as negligent. Deciding not to file a CTR just because it would be late is not negligence. It is intentional and triggers considerations of criminality and much larger fines.
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In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.