I have just transported special freight worth 240,000 GTA dollars and was shown that if I lose but have already delivered a part, the delivered part goes back to the warehouse. I had already delivered the first part and so the second part was destroyed. However, it says now that everything is gone.
When something was destroyed for me it took a while until the load was back. But I don't know exactly which part of the load that was.
But you were lucky that you hardly lost anything. $ 240,000 is quickly farmed again.