You could try to create a third structure with the two other structures as elements.
Not exactly sure this is what you want.
<combined>
<files>
<file id="1">
<data>Some data in file 1</data>
</file>
<file id="2">
<content>Something for file 2</content>
</file>
</files>
</combined>
This will preserve the existing structure and you can save the file as one or as different parts by using e.g.
XElement
.
string combinedData = "<combined><files><file id=\"1\"><data>Some data in file 1</data></file><file id=\"2\"><content>Something for file 2</content></file></files></combined>";
XDocument xdoc = XDocument.Parse(combinedData);
XElement xeFiles = xdoc.Root.Element("files");
XElement xeFile1 = xeFiles.Elements("file").Where(x => x.Attribute("id").Value == "1").FirstOrDefault();
string file1Content = xeFile1.FirstNode.ToString();
XElement xeFile2 = xeFiles.Elements("file").Where(x => x.Attribute("id").Value == "2").FirstOrDefault();
string file2Content = xeFile2.FirstNode.ToString();