.. I mean you can get another reference letter that will mention your position under NOC C and submit it with CSE too,
However, I personally wouldnt do it.. you will just create extra confusion and will make them go through your docs again..
I claimed a position in a company under NOC A only and got a reference letter confirming only that position,even though, a few months before working there under NOC A , I had a position under NOC C.
I had it only in my personal history and thats it. Got my PPR and sent my passport.
If your doc checklist mentioned ref letter only for NOC 0, and you submitted it, then what is the problem? They cant reject you because of it, especially if you mentioned that NOC C position in your personal history.
Just relax!! You are coming up with some random stuff almost 5 months after you submitted your application, and are looking for reasons for them to reject you. C'mon! YOU WILL GET YOUR PPR SOONER THAN YOU THINK!