Please try below code for your requirement...
XDocument xmlDoc = XDocument.Load(filePath);
bool isExists = (from data in xmlDoc.Element("appsettings")
select data).Any();
if (!isExists)
{
XmlElement parent = xmlDoc.CreateElement("configuration");
}
XmlNodeList newXMLNodes = xmlDoc.SelectNodes("/configuration/appsettings");
foreach (XmlNode child in newXMLNodes)
{
child.ParentNode.RemoveAll();
}