Hi Charity
It is the user's course completion records in the course that is archived rather than the course, so the certification notifications should go out correctly.
If the same user is doing the same course that is part of a Program and a Certification then the resetting of the user's course completion from the certification will also reset the same course that appears in the program which is not what you want.
If the same user is able to do the program and certification then it is best to keep them as separate course for the program and certification.
regards