Попробуйте как ниже,
XDocument doc = XDocument.Load(Server.MapPath(xmlfilepath));
Dictionary<string, XElement> CompleteDealSet = doc.Descendants("DealItem").GroupBy(x => (string)x.Element("ID"), y => y).ToDictionary(x => x.Key, y => y.FirstOrDefault());
XElement Selected_Deal = CompleteDealSet[mc_ID];
Dictionary<string, XElement> ItinerarySet = Selected_Deal.Descendants("Day").GroupBy(x => (string)x.Element("DayID"), y => y).ToDictionary(x => x.Key, y => y.FirstOrDefault());
XElement selected_Itinerary = ItinerarySet[dayID];
selected_Itinerary.Element("DayTitle").SetValue(multicentreDay);
selected_Itinerary.Element("Title").SetValue(itineraryTitle);
selected_Itinerary.Element("HotelName").SetValue(hotelName);
selected_Itinerary.Element("Description").SetValue(multidayItineraryDescription);
doc.Save(Server.MapPath(xmlfilepath));