Reg E 1005.11(a)(iii) identifies the "omission" of an electronic funds transfer" as a covered error. The customer made a claim that they should have received a credit, and didn't so this is a claim you must investigate under Reg E rules.
That being said, your investigation will be limited to reviewing your ACH/debit card transaction files. If you do not locate a credit that you failed to process to the customer's account, then you use that as your evidence to deny the Reg E claim.
As a Visa/MC issuer, you also have a contractual obligation to assist your cardholder. Once the Reg E claim is denied, you must also attempt to file a "Credit Not Processed" chargeback on their behalf (if they have jumped through all the hoops for contacting the merchant, documenting the results of the merchant contact, etc.) Since we are operating outside of Reg E at this point, we can require additional documentation prior to filing a chargeback.
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