Thank you very much for your detailed explanations and suggestions. Much appreciated. The swap mode has been suggested a few times before – happy to hear it from you too! And what you describe about all the clones sounds really frustrating. Both points of yours are definitely something we need to come up with a good solution to. These are now entered into our todolist. Thanks again.
As long as your reference footage is made as a sequence of png files, then they will import right into a reference layer in Animation Paper. Did you try that?