Sorry, Meeb, I hadn't spotted your question when I glanced at this thread earlier.
When you revalidate your FI rating by proficiency check, as one of the two required items, the FIE should note that you are dual qualified and, if the revalidation flight check is on a twin, should ask questions on the single during the ground element, and vice versa. That having been done, the CofT should be endorsed SE/ME.
However, under the wierd JAA rules, if you choose to revalidate by experience and seminar you will still revalidate both SE and ME assuming that you hold both qualifications. So, having become a ME Piston CRI (for that is what a ME instructor rating now equates to) you retain the qualification whether or not you ever subsequently instruct on a ME aeroplane. It's just another one of those things that the JAA bureaucrats have let through as a result of not understanding the industry they are legislating for.
Most of the JAA's problems can, in my view, be put down to the fact that the vast majority of members of the various committees are not now and never have been in possession of a pilot's licence. Furthermore, few of the minority that are or have been pilots have been either instructors or examiners and so the FI legislation is even more of a mess than the rest of JAR-FCL. But that's another story.