> I've an application wherein I allow the users to upload stylesheets. I > receive the XSL as a string and hence convert to Xml using the Java > extension I mentioned. I won't have any prior knowledge of the elements > that will contain CDATA sections.
CDATA sections in the stylesheet are always parsed down to ordinary text. Stylesheet processing will discard the CDATA section distinction unless you reintroduce it via the directive in xsl:output. That's normal XSLT operation.