Hi there, Chris,
There's no replace feature. Any time that you want a variation on a synth, you'll need to recalculate the photos positions (this is because the process inherently compares every image to every other image in a collection in order to calculate their positions), however you should note that no photo is ever uploaded to Photosynth twice unless you edit your local copy of the image after it's uploaded the first time.
This means that although when you recalculate the hypothetical office building, any photos used in your previous synths which will also be used in your new version of your synth will not be uploaded, so only the new photos and the new position information will need to be uploaded.
I hope that helps. Feel free to ask if there's anything else you're wondering about or something that I didn't answer.