I am facing the same problem. How long did it take to get the medicals uploaded with the new number?Hope the experience I share will help someone.
Faced similar issue. CIC sent medical request form without IME number. Physician could not link the medical to visa application as IME number was not there. Had to complete medical within 30 days. Sent a mail to CIC and also raised Case Specific Enquiry. Didn't get any response.
At last, sent a mail to Delhi-mc@international.gc.ca
They replied in 12 hours and provided new IME Number![]()