If you keep your plugin data paths the same, you won't have a zillion missing sample messages, or that sort of thing.
For example, I have a zillion projects that have Kontakt loaded into them, and all kinds of samples paths are present for each loaded instrument.
So, when I move everything to a new computer, I always make sure that I set up all my synth content (like Kontakt sample libraries) with the same folder structure, and then all my projects find the samples at the locations specified within the projects.
It isn't the end of the world if you have to locate missing content, but it can be a pain.
Bob Bone