I recently finished a large project with many layers. I was thinking that, in order to resize the project, it might be better to create a back-up copy of the finished file, put all the objects into one layer in that new file, group all the objects, and then resize the one object group. The back-up file with the original layers would allow you to make further changes more easily, if they are needed. And, of course, you just want to back up something that's important.
For resizing or changing the layout of the overall piece, working with one (grouped) object would be better than multiple objects.
Obviously the best thing to do is to think about how big the final product needs to be, or to finalize the layout of objects in a project in the first place. But, I'm betting that people who have a lot of experience with vector programs have run into this resizing/layout change problem before.