You do have to refile and pay the $200 again. Refund will get done automatically due to disapproval.
Email ted.clutter@atf.gov with the disapproved control number and the resubmitted control number. Give it 24-48 hours and he will email you the approved stamp directly.
EDIT: Not sure if you can fix it during the pending phase. Most likely not since it was esigned. Call (304) 616-4500 and ask. That is the NFA branch at ATF.
What he said. Theres no way to fix it once its submitted.