Amazon won't overcharge your FBA Fulfilment or Storage Fees anymore.
Any dimension changes that cause an increase in FBA fees result in an instant alert sent to you. Then simply request from Amazon the reimbursement for overcharges.
Request reimbursement for overcharge of FBA Fees.
If Amazon measures your product incorrectly and overcharges, you can open a case with Amazon and request a "Cubiscan" of your product to re-measure and re-weigh your product. If the findings support your position, you can request reimbursement for the overcharge.