As understood by your post, you missed some dox in your initial application package and sent those missing dox later along with an explanation letter.
If you did not mention your DOB, Country of Birth, (probably) your passport no. then CIC won't take a pain and try to attach 2nd piece of documents to your original ones.
In my view:
Reply to CIC's email stating your DOB, Country of Birth (some other relevant info) requesting again to find the file on the basis of information you are providing in this email.
I hope you get +ve response.
All the best
PS: I also got a same response from CIC when I submitted my new payment form along with an explanation letter. I also missed to mention DOB etc info in that letter, hence I received the same response from CIC.