Let me rephrase what you said so it's a little easier to understand ...
Two different drivers, on two different days, hauled the same shipper's freight, and at their deliveries both loads had shifted cases. The drivers were not allowed on the dock to witness or supervise loading.
Your question is how can you prove the shipper incorrectly loaded the freight?
The answer can be quite simple and apparent, if all the information you have provided is all there is to the story, and given the information presented, the shipper is the common denominator as they were the only entity that had unfettered access to all of the freight.
However, additional information would be helpful. Was the commodity dry or reefer? If it was reefer, was it fresh or frozen? Were the drivers allowed on the dock(s) to witness unloading? Who was the receiver? If it was C&S (Cheat & Steal) in the U.S., then the issue is almost 100% a C&S issue, and never was a shipper problem. Did you examine your drivers' ELDs for hard braking or hard cornering events? Did your drivers get pictures of the shifted freight, or did your team just blindly accept what the receiver was telling them? Were you threatened with a damage claim?
If you are going to accuse the shipper, and demand compensation, which is what I take from your reference to having to pay for the rework, you need to eliminate, with evidence and proof, that no other factor could have influenced the shifted freight. That can be a tough row to hoe.
The minute anyone suggests that some sort of claim is pending, and a rework fee is a claim, everything stops. You have to start documenting as if you were headed to criminal court.