Hi,
you'll need to have two different set of systems, one for editing and one for building. So in your game your player should only reconstruct what you have defined in your "editor". I would actually look into maintaining a flag like "In Editor" or something and if that flag is false, any fsm responsible for the editor side would get destroyed, or the opposie if true you would enable them or something.
also look at completly separating the logic for the editing and "puppet" control your character as you edit it, then it will not make any difference for the character prefab.
bye,
Jean