Transfer will pop up dialog boxes to ask you questions about these things, if you start an import and there’s a choice to be made (because samples in your project to be imported duplicate some already on the plus drive).
It will automatically assume you want to finish up with a working project, by importing samples where necessary, but will offer you choices before doing that. If you choose the re-associate existing samples on the plusdrive it will do that.
To be completely sure it’s going to do what you want, best do a couple of experiments based on a throwaway project, sample, and sample folder.
I’ll do a COMPLETE back up of all Projects, Samples and Sounds, and that way I should have everything on my Computer if something goes missing when re-importing.