from previous answers to similar threads, it seems you will get the miles for your original paid ticket (CW).

The special offer at checkin comes with no extras, and this is hardly suprising given that $400 to upgrade is super cheap and therefore you cant expect miles/points as well. If you had upgraded to F at the ticket desk you would have got the miles etc but had to pay about $2000 USD for the priviledge.

So, don't get your hopes up