Here is a sample function that you could use to save the comments. It allows you to edit one key/value pair at a time. I've also added some stuff to format the file nicely based on the way I commonly use the files (You could easily remove that if you want). I hope this might help someone else in the future.
public static bool setConfigValue(Configuration config, string key, string val, out string errorMsg) {
    try {
        errorMsg = null;
        string filename = config.FilePath;
        //Load the config file as an XDocument
        XDocument document = XDocument.Load(filename, LoadOptions.PreserveWhitespace);
        if(document.Root == null) {
            errorMsg = "Document was null for XDocument load.";
            return false;
        }
        XElement appSettings = document.Root.Element("appSettings");
        if(appSettings == null) {
            appSettings = new XElement("appSettings");
            document.Root.Add(appSettings);
        }
        XElement appSetting = appSettings.Elements("add").FirstOrDefault(x => x.Attribute("key").Value == key);
        if (appSetting == null) {
            //Create the new appSetting
            appSettings.Add(new XElement("add", new XAttribute("key", key), new XAttribute("value", val)));
        }
        else {
            //Update the current appSetting
            appSetting.Attribute("value").Value = val;
        }
        //Format the appSetting section
        XNode lastElement = null;
        foreach(var elm in appSettings.DescendantNodes()) {
            if(elm.NodeType == System.Xml.XmlNodeType.Text) {
                if(lastElement?.NodeType == System.Xml.XmlNodeType.Element && elm.NextNode?.NodeType == System.Xml.XmlNodeType.Comment) {
                    //Any time the last node was an element and the next is a comment add two new lines.
                    ((XText)elm).Value = "\n\n\t\t";
                }
                else {
                    ((XText)elm).Value = "\n\t\t";
                }
            }
            lastElement = elm;
        }
        //Make sure the end tag for appSettings is on a new line.
        var lastNode = appSettings.DescendantNodes().Last();
        if (lastNode.NodeType == System.Xml.XmlNodeType.Text) {
            ((XText)lastNode).Value = "\n\t";
        }
        else {
            appSettings.Add(new XText("\n\t"));
        }
        //Save the changes to the config file.
        document.Save(filename, SaveOptions.DisableFormatting);
        return true;
    }
    catch (Exception ex) {
        errorMsg = "There was an exception while trying to update the config value for '" + key + "' with value '" + val + "' : " + ex.ToString();
        return false;
    }
}