C# Удаление ссылок и использования пространства имен из данных XML

Минимальный воспроизводимый пример не приведен. Вот общее решение на основе XSLT, которое будет работать с любым правильно сформированным XML-файлом.

Входной XML

<root>
   <ns2:AppHdr xmlns:ns2 = "some stuff">*contents of the header*</ns2:AppHdr>
   <ns3:Document xmlns:ns3 = "some other stuff">*contents of the document*</ns3:Document>
</root>

XSLT

<?xml version='1.0'?>
<xsl:stylesheet version = "1.0" xmlns:xsl = "http://www.w3.org/1999/XSL/Transform">
   <xsl:output method = "xml" indent = "yes" omit-xml-declaration = "yes"/>
   <xsl:strip-space elements = "*"/>

   <!-- template to copy elements -->
   <xsl:template match = "*">
      <xsl:element name = "{local-name()}">
         <xsl:apply-templates select = "@* | node()"/>
      </xsl:element>
   </xsl:template>

   <!-- template to copy attributes -->
   <xsl:template match = "@*">
      <xsl:attribute name = "{local-name()}">
         <xsl:value-of select = "."/>
      </xsl:attribute>
   </xsl:template>

   <!-- template to copy the rest of the nodes -->
   <xsl:template match = "comment() | text() | processing-instruction()">
      <xsl:copy/>
   </xsl:template>
</xsl:stylesheet>

Выходной XML

<root>
  <AppHdr>*contents of the header*</AppHdr>
  <Document>*contents of the document*</Document>
</root>

С#

void Main()
{
   const string SOURCEXMLFILE = @"e:\Temp\input.xml";
   const string XSLTFILE = @"e:\Temp\process.xslt";
   const string OUTPUTXMLFILE = @"e:\temp\output.xml";

   try
   {
      XsltArgumentList xslArg = new XsltArgumentList();

      using (XmlReader src = XmlReader.Create(SOURCEXMLFILE))
      {
         XslCompiledTransform xslt = new XslCompiledTransform();
         xslt.Load(XSLTFILE, new XsltSettings(true, true), new XmlUrlResolver());

         XmlWriterSettings settings = xslt.OutputSettings.Clone();
         settings.IndentChars = "\t";
         // to remove BOM
         settings.Encoding = new UTF8Encoding(false);

         using (XmlWriter result = XmlWriter.Create(OUTPUTXMLFILE, settings))
         {
            xslt.Transform(src, xslArg, result, new XmlUrlResolver());
            result.Close();
         }
      }
      Console.WriteLine("File '{0}' has been generated.", OUTPUTXMLFILE);
   }
   catch (Exception ex)
   {
      Console.WriteLine(ex.Message);
   }
}