Yes, they did. On the website it said to attach your 'AOR' in the 'Letter of Explanation' section when uploading the documents.
When you submit your application, you must provide all supporting documents listed in your document checklist. You must also include a copy of your Acknowledgment of Receipt letter from CIC.
If you apply for your work permit online through MyCIC, upload the above document(s) in the Letter of Explanation slot in the document checklist.
Website: http://www.cic.gc.ca/english/work/permit/extend/permanent.asp
I suggest you send them a Case Specific Enquiry (including your AOR) immediately.