As far as I know, checklist have been the same. your friend should ask her representative for the email/correspondence that IRCC sent, to confirm if an application number was really given. If there is really an application number, then she can always use that as a reference to ask for an update or by just merely checking through ECAS.
Anybody can correct me, but I haven't read anything that somebody gets an application number, if their application was returned. You'll only get an AOR1, if your application is complete. If it's not, they'll return it, then they'll only give an AOR, once you complete the requirement. If they are doing the sending of scanned copies of your application, then letting you know through that email of the deficiencies, the more that your friend should ask her representative for that email. so she can confirm what's happening. I think that is her right to see all the email correspondence from her rep.