I really doubt whether IRCC officer would have missed the passport. In fact, they are expecting those scanned copies from each applicant. I am about 100% sure they would have received and updated it. Most likely, the agent doesn't know what he/she is saying. In fact, IRCC will reach out to an applicant towards the 30 days to ask for it again! Nevertheless, nothing is impossible with IRCC.
What I would suggest is that you send them an email to confirm receipt. They most likely wouldn't reply on time and may not even reply at all. But if they do (they replied to mine after about 1 month), it will help you relax. Also, you can also order your ATIP notes. It was stated in my ATIP note that the scanned passport was updated the next business day after I emailed it to them.