You can parse the existing XML file into DOM and append new elements to the DOM. Very similar to what you did with creating brand new XML. I am assuming you do not have to worry about duplicate server. If you do have to worry about that, you will have to go through the elements in the DOM to check for duplicates.
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
/* parse existing file to DOM */
Document document = documentBuilder.parse(new File("exisgint/xml/file"));
Element root = document.getDocumentElement();
for (Server newServer : Collection<Server> bunchOfNewServers){
Element server = Document.createElement("server");
/* create and setup the server node...*/
root.appendChild(server);
}
/* use whatever method to output DOM to XML (for example, using transformer like you did).*/