I don't know exactly what you want to do, so it's a little difficult to give you a specific answer, but here is a piece of code that will hopefully be of some help. It locates the proper comment through its Prompt sibling, then perfoems a string substitution on it. Alternatively you could replace completely the CDATA section in the element by doing $response->set_cdata( 'your text here').

Note that there might be a bug in the released version of the module (the root start tag might be output twice, at least that was the case with the development version of XML::Twig) so you might want to grab the latest bestest version (dated June 23) from xmltwig.com