Hi Paul,
Probably the way I'd do it is through an XSL transformation. That's a good way of translating between different XML applications; you write an XSLT file, pass it along with the XML input file, and the XSLT processor outputs the translated XML file.
You'll need to create an XSL stylesheet, and then pass it through an XSLT processor. LabVIEW can't do the transformation though, so you'll need to use an external one. I remember using command line tools that do it, that just take the two input files as arguments and the output file is produced. Or you can do it programitcally, although I haven't done it in Java, just .NET languages. In .NET, it just takes a few lines of code (three or so?), and I'm guessing with a Java base processor (Xalan-java perhaps?) it's just as easy.
A beginner might be tempted to do the transformation by manually traversing a DOM and picking out elements with lots of if..then...else... but this can be tedious and error-prone.
Hope this helps!
- Alex