On our August '03 trip, we checked in to a Contemporary wing room with the 7-for-4 plan. The room was dirty (*I* noticed the cobwebs hanging from the ceiling and I'm typically far less sensitive about these things than my wife) and when the bed rail arrived it had nasty stains on it. It was clear to me that my wife was *not* happy and other factors made it obvious that getting another room wasn't likely to solve our probelms. I don't want to Contemporary-bash any further--that was over 2 years ago and some of the issues were just matters of personal preference (i.e. the decor).
In any case, we tried to get in to the Concourse Steak House, but the wait was supposed to be about an hour and we where HUNGRY. So we went to guest services and checked to see if there were any priority seatings available at Narcoosee's. There were--but for about 5 minutes from the current time. The cast member said that we wouldn't make it but I asked her was the grace period was before a PS got cancelled. "15 minutes," she said. "We'll make it," I said.
After a nice dinner at Narcoosee's, I stopped at the desk and asked if they had any rooms available. They didn't for that night, but could get us in the next day. I asked if he could check the Polynesian because we didn't really want to stay at the Contemporary even the one night and didn't want to have to change hotels the next day. He went in the back and when he came out he said he had found a room for us.

We took the monorail back to the Contemporary, put our bags in the rental car and drove over the the GF to check in. We didn't even have to check out of the Contemporary. We were charged the difference in the rate between the two rooms so we paid exactly what we would have had we booked at the GF to begin with. (And if I recall correctly, there was no availabilty at the GF or the Polynesian for those travel dates when we originally booked.) The only -- and very minor -- inconvenience was that we had two cards. Our UPH's were on our old Contemporary key cards and we got new key cards for the room at the GF.
Also, if that last part of your stay is a room-only reservation, isn't the cancellation period 48 hours as opposed to the 5 day period for Travel Company packages? If it's booked as a WDTC package, can you rebook as a room-only reservation at this point in time? I'm pretty sure that if you change Disney resorts for those last two days, they won't penalize you--especially if you're upgrading. (I don't know that you are....)
As for the discounted rate.....I think it could end up depending on the type of discount and/or the cast member helping you. Many codes apply only to a certain number of rooms and I could them having rooms available but not at the discounted rate--just like you find when we call to make reservations. But I also wouldn't be surprised if it's either a set Disney policy to extend the discounted rate once you've checked in or done solely at the cast member's discretion. I suspect that any of the resorts' individual managers would rather extend a discount and have their occupancy rate higher than have you switch to another resort.
In our case, not only did the GF have one more room filled, but overall, the company got a few hunderd dollars more of our money.
Brett