I am thinking what will be the mental condition of your CO when he will get the first e-mail, upload everything to the server and may be 2-3 days later will get the 2nd e-mail. He now have to figure out what to do with the files he uploaded in the first time. Think how much time he have to waste to figure out what is what now.I sent two emails. One with subject of ONLY "PGP-APR" and another with "PGP-APR and application number". I hope they pick one of it.
Dilemma with emails is you will never get acknowledgement so you never know when they will pick and update myCIC.
Its only a waiting game.