Say Team Magma's Secret Base and Mimikyu with "Shadow Box" Ability are both in play. If I put Dedenne GX on the Bench, can I use its "Dedechange" Ability or will it be blocked because it has damage counters on it?
Since Dedechange and Team Magma's Secret Base are simultaneous effects, it is up to the player to choose the order in which they will be applied.
DedechangeShadow BoxTeam Magma's Secret Base