Welcome to FT, leekman and our corner of the forum!

Just to straighten out your timeline:

1 - booked flights, then cancelled
2 - two days later, when refunds are calculating how much to give you, the tickets turn out to be non-refundable and therefore only tax is due to be returned
3 - at this point, you cancel the refund
4 - 7 days later, EK try and confirm the original booking but the original fare class is sold out, so they have put you on a waitlist

In airline reservation systems, each fare class has a limited number of seats, and an associated waiting list. If by any chance the revenue managers decide to increase the number of seats in a particular fare class for sale, they will be able to see that you are on the waiting list and confirm your booking/seat at no additional cost.

In practice, generally revenue managers have very limited discounted seat capacity (as your ticket was, as it was non-refundable). Once the discounted seats are gone, they are usually gone. If it turns out on the day you are not able to fly as your fare class is still not available, you will have the option of a refund - which in your case will only be the tax paid - or changing the fare to class to one which is available, which will incur the change fee.

In order to have the best possible chance of getting on the flight, or at least, receiving compensation in the event you are denied boarding, you will have to pay to upgrade your ticket to the new fare class (which will be the fare difference plus the change fee). Do check the cost of making a brand new booking, which might turn out to be cheaper than the fare difference and change fee!

Also, I do recommend you check the fare conditions before purchasing for the full list of change/refund penalties!