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.
Source: TPCi Rules Team (2021-04-08)

Relevant cards

Note: All applicable cards may not be listed below.
SM10_57
SM10_57
SM12_97
SM12_97
DC1_32