To reproduce: Make shipping container (my test was 3x3x7) with a threshold switch glued to the side. Insert 1 stack of items (I used a brass funnel) and observe the threshold switch. It should have a bright red bar in the fill meter on the side. Assemble the vault onto a gantry contraption and move it (Mine moved 5 blocks). The threshold switch now reads completely empty.

I had the exact same issue with mechanical pistons. As soon as I moved it all the items were gone. Good thing I wasn't in survival.