I've not heard any sense on the subject, but a friend hit the same problem and I know the club has submitted a couple of applications with the same score entered in both sections for the exams that have now been split. Apparently 'The CAA seemed OK with that'.
Given that no one seems to have access to the new papers yet either, it's not like there is another option. I'm feeling very lucky to have squeezed in before the JAR deadline now.
Ian