i think you need to make the changes through dev studio only.
Yes pawan.. i made dummy changes like moved 1 element up/down and saved WSDL. then it started showing updating values in XML.
But its a bit strange.. should pickup updated values automatically after cache flush. because we can create a request with newly added values without refreshing wsdl. but to update xml we have to update wsdl.
Yes, it might be because the WSDL generated from the developer studio generated on the basis of the field mapping as you defined in that Web service hence if you will modify the XML code manually then it won't work as this is not matching with the mapping of fields for that WSDL defined in Dev studio...
moreover experts can suggest you for the most correct answer