While it appears that the counter advances when you netfile, it actually advances when you go from the order confirmation page to the netfile page.  So that if there is an error and you cannot netfile, it will advance the counter a second time for the same return.  

If you are ready to go to netfile for the second time, call them. They phone back in less than 5 min.  They will say that it won't charge twice but it does.