the only change, if they do use the Chicago set, will be the proscenium. the 1st tour has barely any proscenium at all (compared to other sit downs, espicially when it comes to those side balconies) they were added to the Chicago set specifically, (since the chicago set is the original touring set, they build a new touring set to continue on, chances are they will not be used on the 2nd tour (since they are not used on the 1st) and usually when there is a 2nd tour, it is somewhat smaller just so it can fit into more theatres, but the differences are hardly noticeable.
it probably will only be noticeable for die hard fans of the show, or people who are used to seeing the show in Broadway. Honestly for me it was a big dissapointment when i first saw the tour.
http://www.flickr.com/photos/27199361@N08/ Phantom at the Royal Empire Theatre