From a business-that-needs-to-make-money standpoint, you messed a couple things up here:
It was FBA. The customer was going to get a refund for the lost package ANYWAYS when they reported it to Amazon. Since you manually refunded, in the event the customer claimed non-receipt to Amazon directly, they would have initiated a refund from your account to the customer, and 45 days later you would have received a sale credit from the lost item. At this point, Amazon has no way of knowing that they need to take responsibility for the lost item, so they won't be initiating the automatic credit to you. You lost money there. Don't refund manually for FBA orders of this caliber.
The next is responding to the customer issue directly to the customer. The reason you use FBA is because they provide the customer service for you. There is no need to contact the customer directly for lost packages. Merely direct them to Amazon's customer service.
The last bit is that Amazon will remove the negative feedback if it is an FBA issue. These are struck through, as you saw, and will NOT count against your ODR, since you are not at fault. If you still see the negative affecting you, then it will take a few days to fall off your charts.