One box of two missing

[arctictulsa]

I sold an item that ships in two boxes. According to FedEx, both boxes were delivered at the same time, but my customer says one box is missing. The customer opened a return request saying the item is missing parts or pieces. 

The part the customer says he does have is a lid, which we also sell individually, so I told him he could return it for a partial refund, but he needed to pay the shipping since he stated the lid was not defective. For the other box, I told him he should file a claim with his homeowner's insurance for the stolen item.

His response was "I will return lid I will pursue matter with eBay since u refuse to resolve"

I'm sympathetic to his situation, but I'm not responsible for what happened on his property after a successful delivery.  

Should I wait until the time runs out on the request (there's no way for me to say I refuse the refund)?

Can I accept the return then when he only returns the lid, only give a partial refund?

Can I somehow beat the customer to the punch and contact eBay about it first?