Depending on where you are in your retargeting workflow, you can bake the retargeted animation either to the target character’s skeleton or Control Rig.
Typically, you bake animation to the target character’s Control Rig when you no longer need the live link between your source and target characters, and you still want to make some adjustments to the retargeted animation by animating the Control Rig.
You can bake animation to the target skeleton when you finish making all adjustments to the retargeted animation and are satisfied with the results.
To bake retargeted animation to the target character
The retargeted animation plays in the scene as Maya bakes to either the target Control Rig or skeleton. For each frame of the retargeted animation, Maya sets one key on each effector or joint.