When you first enter a NV2 set of books, you are prompted to run Default setup which sets up the windowing system within that database so you do not have to click on each folder and sub folder within your NV2 books tree. Default setup does not setup the report windows. The report windows and system windows will be setup once you visit the folders/sub folders for the first time.
Once default setup is complete, NV2 informs you to backup the workstation folder after NV2 shuts down. The windowing structure of the books is stored in the workstation folder (for example C:/nv2/workstation) which includes the path and name of the books. If you copy/paste the books to N:/MYBOOKS from C:/NV2/MYBOOKS you will be asked to run a default setup again as the path is different. Default setup needs to be run only once.
I assume you are running the lastest version of NV2 (2.04).