Wait until the tracking has updated and the item not received case has closed.
Then send a partial refund - you can use the reason 'postal discount'.
It is expecting you to fully refund because of the open case.
"There are two ways to be fooled. One is to believe what isn't true; the other is to refuse to believe what is true.”
Søren Kierkegaard, Danish philosopher (1813 - 1855)