Found the solution. I use fs.SetLength(0) to set the stream to empty and then I save back the XML into it.

VB Code:
  1. Public sub UpdateControl()
  2.     Dim Doc As New XmlDocument
  3.     Dim fs As FileStream
  4.  
  5.     Try
  6.       fs = New FileStream(_BatchListFile, FileMode.Open, FileAccess.ReadWrite, FileShare.None)
  7.       ' Load the XML through the filestream
  8.       Doc.Load(fs)
  9.  
  10.       ' Pick up node using SelectSingleNode and update
  11.  
  12.       fs.SetLength(0)   ' This clears any previous data from the file
  13.      ' Write back the Xml file
  14.       Doc.Save(fs)
  15.     Catch ex as Exception
  16.       throw new Exception("", ex)
  17.     Finally
  18.        if not(fs is nothing) Then
  19.          fs.close
  20.          fs = nothing
  21.        End If
  22.     End Try
  23. End Sub