Mastercard and Visa rules on debit card claims against merchants operate independently of Regulation E. The bank must comply with both sets of rules, once based on the regulation, the other based on the card association's rules.
The bank believed it had evidence of the customer's authorization when it closed its investigation after 90 days and revoked any provisional credit it may have given. That's when Regulation E's coverage ended, but the Mastercard or Visa rules allowed for further action by the merchant, and the merchant took that action when it submitted a merchant credit. The card association rules require that such a merchant credit be credited to the cardholder's account by the issuing bank. That is not in conflict with Regulation E.
If the facts were reversed, and the bank had provided the customer a final credit under Regulation E, but the merchant later, and within card association timelines, resubmitted the debit, the bank would not be able to reopen the Regulation E dispute even if it has to honor the merchant transaction.