Depending on where you are in your retargeting workflow, you can bake the retargeted animation either to the target character’s skeleton, Control rig, or Custom rig.
Typically, you bake animation to the target character’s Control rig when you no longer need the link to your source character or, for example, if you want to export the rig to MotionBuilder. (See Send HumanIK rigs to MotionBuilder.)
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 animation bakes to either the target skeleton, Control rig, or Custom rig. For each frame of the retargeted animation, Maya sets one key on each effector or joint.