You don't 'apply a discount' to an existing booking, you effectively make a new booking with the same reservation number. So you can choose from whatever discounts are available later, and switch to any of them if they appeal to you. It's actually kinda irrelevant whether you even have an existing booking at that point - other than the more people who make tentative bookings, the less likely any given room category is to be included within offers. Disney will only offer discounts on unsold rooms that they are having trouble filling - if an area is already mostly booked with tentative reservations, they won't offer many discounts (this often happens with POFQ, and sometimes POR, as they are very popular resorts).
It will probably be done by then, but it's too far out to even guess if the work will overrun (they haven't even started yet!). I'm wondering if they might delay the start of works until the POFQ children's water play area is completed, rather than having both kids' pool areas out of action at the same time, which has been delayed until mid-January (it was originally due for completion on 24 Dec).
Whichever though, I really wouldn't worry about it very much either way as there are five alternate pools around Riverside alone, plus the pool at French Quarter if having access to a water-slide and hot tub are the be-all and end-all of your vacation plans. Also there will be effectively be no construction work visible, as the POR feature pool is located on its own isolated island surrounded by trees, it's very secluded. It'll probably be about the least significant construction impact of any resort pool.
Andre