Penalty for late shipment- resolution and reversal?

[nelcon44]

On my seller performance, I've been penalized for late shipping for two unusual situations:

1.  A buyer was purchasing four items that were ending at various times over a 3 or 4 day period.  He asked me to hold on shipping until all items were purchased, then ship them together to cut the cost of shipping.  He paid for the items as the auction ended (including shipping for each separate item), but on the last item, I made a discount on the invoice to reflect the shipping cost savings.  I've been penalized for late shipping on the items which I was holding for shipment.

2. In another case, the item being sold was a complicated model railroad kit.  After the kit was purchased, when I was packing it for shipment, I realized there were no instructions for construction of the kit in the box.  I contacted the buyer, and offered to send him the kit for the cost of shipping only.  He wanted me to do that, so I refunded the cost of the purchase, and sent the kit to him.  This obviously delayed the shipping time.

How do I get these penalties reversed so my seller rating is not degraded?