It will only delete one and not a stack. The reason this happens is because you get an item you didn't already have in your inventory from the package, so it pushes everything over by one slot.
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I didn't get any new items that I didn't already have in my inventory. I did get one extra enhancement core, but that shouldn't have caused it to rearrange. In D1 you could dismantle an entire stack of cores at one time. I haven't found any evidence one way or the other to prove how it works in D2.