One potential workaround I've thought of in the context of Polymer Designer, is to patch up Polymer() to be able to able to redefine elements - possibly by inserting an extra prototype in the prototype chain just about the instances, then on redefinition change that object's proto pointer to the new prototype and skip calling document.registerElement(). I'm not all all sure what might break if I did that, but I'm pretty sure something would. The fallback is to just reload the page, and try to serialize the important state in some way.
-Justin