The EU OPS questions were there because that's the current legislation. Despite the fact that the current syllabus refers to JAR-OPS the CAA decided to 'get in the groove' by deleting references to JAR-OPS 1 and replacing them with EU OPS. It caused a great deal of confusion. All the answers were the same as before, though.
Should you do the new syllabus or old? Most FTOs teach a combination now anyway and include topics like diesel engines which are from the new syllabus. Certainly OAT do, as do we. I would think you should avoid the new questions if you can, as there will be lots of them and they won't be validated properly. As the CAA are talking about running the two exam systems in parallel for a while it should mean that when they make a formal announcement, which they haven't done yet, they'll set a date and say anyone who starts an ATPL course after that date will be on the new question bank. I'd expect at least three months notice of the date.
The best decision would be to introduce the CQB15 questions gradually after the DEC 09 start date, rather than all at once. With a bit of luck that should allow the FTOs to keep on top of them.