I'm not aware of a built-in way to delete specific embedded xml files so you are going to need a macro to loop through your files and delete any on command. Try this macro
Code:
Sub CleanupXML()
Dim aCX As CustomXMLPart, iResponse As Integer
For Each aCX In ActiveDocument.CustomXMLParts
Debug.Print aCX.NamespaceURI
If Not aCX.BuiltIn Then
iResponse = MsgBox(aCX.NamespaceURI & vbCr & vbCr & aCX.XML, vbYesNo, "Delete this one?")
If iResponse = vbYes Then aCX.Delete
End If
Next aCX
End Sub