The reconciliation and the credit-card due date are separate risks. A pending complaint does not automatically stop interest, late charges or reporting. If the due date is approaching, contact the issuer through an authenticated channel and ask for written instructions. Where you can safely afford it, paying the undisputed amount or making a clearly documented protective payment may reduce delinquency risk, but it can also create an excess-credit situation—so keep the two payment references separate.
After resolution, inspect the next statement. Confirm the value date of the credited payment, any late fee or finance charge that appeared because of the failed transaction, and whether a duplicate payment remains as a credit balance. Challenge only the entries that are actually incorrect; do not mix a failed-payment complaint with unrelated statement disputes.