I suggest you conduct a documented review of the activity in the account and, if justified, file a DEP now. That filing will be retroactive for CTRs in the last 30 days and will at least "stop any bleeding."
Do not automatically backfile the missing CTRs. You will need to seek a
backfiling determination from the IRS.
Don't worry, if you were the only bank to ever do this, they would not have an established procedure for fixing it.