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If I have Shockwave in play and my opponent has 2 characters with 1 damage left each (say Optimus Prime - Battlefield Legend with 13 damage and Nemesis Prime with 15 damage) and I play System Reboot forcing them to discard 2 cards, can they choose to put both damage on Nemesis Prime or must they put 1 damage on each?

Each card discarded creates a new instance of 1 damage, so they will be forced to put one damage on each.
Source: Wizards of the Coast (2019-02-11)    【Link to Ruling】
Tags: Decepticon Shockwave, Cybertron Commander