Guys, I also submitted a 2nd application last year (because Canada post did not get proof of delivery for the 1st app). I wrote a cover letter explaining the situation and asked them to return one(both apps were complete). I attached a print out of the same fee receipt. Turns out they received my 1st app and processed it. They never returned the 2nd one.
So I think lana is fine having sent a 2nd app. Chances are they will look at the 1st one that was received, if it's incomplete, it will be returned. If the 2nd app is complete, it should be processed.