I asked the question about the LS-Dyna Restart module because I tried to emulate the exact same test I outlined above. I had some problems in that even after applying a full restart and flipping the boundary conditions my results are exactly the same. Here is my Project Tree:

Here is the First simulation set up and results: 

And here is the restart simulations set up and results: 

As you can see it has just reexecuted the boundary conditions from the first simulation. Please could you advise on performing subsequent simulations with differing boundary conditions?