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.
CanadaPRWaiting said:
I have sent the reuqest about my application whereabout, and i also sent additional docs later. My initial application sent on 29th May 2013. Additional docs reached on June 28th. Can you explain me what this mail says?
Dear XXX,
This is in reference to your recent correspondence concerning your Application for Permanent Residence in Canada under the Federal Skilled Worker Program.
Presently, we have no record of your application in our database; therefore, your IMM 5406 as well as the copy of the birth certificate for your spouse have not been retained.
Thank you for your interest in Canada.
CB
Client Service Unit
Citizenship and Immigration
Centralized Intake Office
Sydney, Nova Scotia, Canada