Unfortunately, I don't have that choice. Briefly, remember that I mentioned
that work is done on the result from script A. This is done by a Java
programs (not own by us) that 'swallowed' the <foo> because it is not
'recognized'. I don't want to go into details about this since I can't change
that.

Any other ideas?

Get the intermediate Java programs fixed or replaced, alternatively
quit your job. The kind of hackery you seem to require is the root
of many a maintenance nightmare.  Do you really want to get through
all the complicated code to find a small bug, or the change necessary
because the Java programs now swallow another piece of data, or to
check where a new element from the source got lost? Stress shortens
your lifespan.