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If I had a team with Omega Supreme and Decepticon Skrapnel and someone attacked my Skrapnel for 15 damage but because of his ability (can only take 3 damage) Does two of those 3 damage go over to Omega Supreme? Therefore Skrapnel will only take 1 damage?

Yes, you can choose to allocate the attack damage that way in this scenario.
Source: Wizards of the Coast (2019-05-17)    【Link to Ruling】
Tags: Omega Supreme, Autobot Defense Base