When LHDN or the portal returns a query, teams often patch the field named in the letter and resubmit. The original application is not reconstructed. A second error—related, sitting one schedule over—travels in again.
Take the submitted pack out of email and screenshots. Rebuild what went in. Compare it to source. Then review the amendment as a new application, with the same completeness bar you should have used the first time.
That second read is the cheapest part of an otherwise expensive exception. It also leaves a file note your board or internal audit can understand without sitting in the portal.