Of course you should re-register in old course even if you have completed any 1 subject in the pending group. There is just one problem the deadline for registration (or re-registration) due by 30th June has already gone and if in your case re-registering becomes due at any time in the near future then there is a possibility that ICAI will only grant fresh registrations in the new course only. Why I am saying this is because in the recently released 57 FAQ's on the new course, Re-validation (read Re-registration) at Intermediate level is covered and Final level is not yet covered. And till date no other notification has been released to provide more light on this situation by the ICAI. People will speculate that the ICAI will grant re-registration in old course only to Final students as well but it can't be said over till it’s actually over.
Still if you get the chance stick to the old course. I can also substantiate my answer with another insight. If you remember when P.E.II was changed into Finals, then the first attempt as per the new curriculum then was quite tough and only after 2-3 attempts a saturation point was achieved were level of exams went a little down and knowledge of students went a little up. So what I suggest is even if you have not started preparations of the pending group re-register yourself in the old course and wait for the first attempt and see the level of exams, in the meanwhile prepare the common topics as per the old course.
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