I have an FBX subnet which contains an animation free rigged character and another FBX subnet that contains an animated skeleton of the same character.

How can I apply the animation from the animated FBX subnet to the character subnet? Is there an easy way to do it or do I have to write a script to link all the attributes from the animated subnet to the un-animated one?

Are the nodes named the same inside the subnet? Because you could use chops to fetch all the channels under one root, and then export them with a different root.

Yes they are. The un-animated subnet has a few extra nodes (skin geo etc.) but the hierarchies and names of the skeletons are the same. Unfortunately chops is very much a weak point for me in Houdini. How could I go about doing what you have suggested?