In total, you can request 2 FBA fee reimbursements for the same item.
The first time, try requesting reimbursement for only 1 order. The reimbursement amount will be small and usually, Amazon will acknowledge their mistake and reimburse you.
After they confirm that they're going to reimburse you, open the 2nd case and submit the remaining orders from the list and point out the fact that Amazon has already acknowledged their error and reimbursed you already for the inaccuracy.