I called CIC (finally got through to them) and asked if they received the docs on time. They said yes, they received them the on the day I submitted and that the officer should have seen them. They were submitted on the deadline day. Things proceeded without any issue. Got an update on my application about 3-4 weeks after submitting the docs, asking for the medical exam.
I don't know the details about your issue, but if it's exactly the same I faced ("overdue" but still within deadline and still able to submit), then I would say you should be ok as long as you submitted on time. I hope that helps. You can also try calling CIC (you may need to try multiple times to get in the queue) just to put your mind at ease a bit more.