It isn’t complex really. But there are details to understand. wM IS does a lot of things for us but we still have to understand how IS parses XML to create the corresponding document var.
The screen shot is nice for showing what steps you’ve defined. What is not shown, and what may be the underlying issue, is what exactly is happening at run-time. The MAP step you shared shows what you’re expecting the document in the pipeline to look like. But the suspicion is that it does not look like that during execution as @engin_arlak and I have noted. If the response from the called endpoint is indicating that the q1:GOVR_C value is null by using the xsi:nil=“true” attribute, q1:GOVR_C will be a document, not a string.
Use the debugger to step through this and share a screen shot of what the document looks like in the pipeline. You might also be able to see/capture what the XML string that is returned from the SOAP call, though that may be hidden from view.
Side note: the use of clearPipeline in multiple places is a little suspect. Not a real problem per se but something to consider avoiding. Search for “clearPipeline” in the forums and you’ll find various discussions and viewpoints, including Use of ClearPipeline in the flow services. The guideline we follow is to explcitly drop vars as soon as they are no longer needed. Use clearPipeline judiciously and only to help protect against “bad” services that create “pipeline litter” – vars that are not declared as output.