Cameron White

You can likely do this purely in SOPs using Agent Animation Unpack (output either a single motionclip, or a set of packed motionclips), and then use the Agent Clip SOP to import these into the other agent definition

In Python, there is a hou.AgentClip constructor that lets you make a copy of the clip for the other agent definition's hou.AgentRig

These both would require having matching skeletons / joint names for the joints that you want to copy animation between

I think you could also likely just use the rest pose directly, rather than merging it into the capture skeleton

The input to the Agent from Rig SOP is just used as the agent's rest pose (e.g. the pose used as a fallback when there isn't any animation assigned to the agent) and doesn't need to be the capture pose
The capture pose can be wired into the third input of the Agent from Rig SOP when adding a shape

Just a guess, but the capture pose output from FBX Character Import doesn't necessarily include all of the skeleton's joints, just the ones used for skinning
If that's the case, using it as the input to the Agent from Rig SOP means that the agent's skeleton will be missing some joints, which could explain animation issues