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When a Combiner combines and the upgrades on its components go onto it, does that count as putting it on a character in the same way that Swap Parts does? For example: Torox has Energon Slingshot before Predacon Enigma was played. When Predaking is combined into, will Slingshot count as being put on a melee character and have its ability to deal 1 damage activate?

No. Upgrades are not “put on” when Combining, they are “kept on”.
Source: Wizards of the Coast (2019-03-08)    【Link to Ruling】
Tags: Combiner