ok..
you meant you changed the major/course but still study same length of time and have a diploma/degree.
(if you elaborate your situation more, I would have understood correctly from the beginning)
don't think it would be problem, as long as you finished your course and have a diploma.
is your course/major name on your study permit?
If so, write a letter explain why you change your course with your PGWP app. (obviously your confirmation of degree would be under different program).
otherwise, you do not need to inform that to CIC.