When you check in, let the front desk person know that you have two reservations. They can "connect" them and if available, they could give you an upgraded room for your entire stay.

Normally, if you are in the same room type for both reservations, then the hotel staff should be able to let you keep the same room for your complete stay. But since you have two different room types they may not be able to accomodate that.

Now, what I would suggest is to keep checking award availability for that last night. A base room award may open up. If it does, grab it. You can then cancel your upgraded room night. (I'm assuming the cancellation policy will allow you to cancel with no penalties.)

You can also contact the hotel's GM (call or email) and ask if they can help you out. They may be able to open up a base room for you on that last night, thus saving you the paid night. Or the GM may be willing to pre-upgrade your entire stay to the higher level room (or possibly even higher) without any extra charge to you. It is worth asking about at least.