Unfortunately, this is out of our hands. Flying Saucer basically
starts from a DOM Document instance. As a convenience to our users, we
provide basic integration of the XML reader APIs that ship with the
JDK, so that either the JDK XML parser, or another one implementing
those APIs, can be used. But if there are problems with the parsing
you need to figure this out outside of FS. My guess is you should use
a very forgiving parser, perhaps Neko or TagSoup, see if it skips over
your problem, and then use some XSL magic to wipe the script element
from the input.
When we have a DOM Document we do indeed skip any script elements in
that Document.
Sorry I don't have a better answer for you.
Best,
Patrick